Wow. I "stumbled across" [hehehe] this a year later and am quite entertained.
I'm confused at how Maxperson was right that you can't use a reaction to avoid the thunder damage but for the wrong reason. The term "instantaneous" is D&D jargon with a specific meaning not to be replaced by dictionary definitions just like words like "attack." Mechanically, instantaneous duration simply means the spell acts then is gone even if its effects continue, so those effects can't be dispelled. It has nothing to do with how fast the magic actually happens. Look at acid splash. The caster conjures a bubble of acid and physically "hurls" it at a target which can make a DEX save. It's not like pointing a finger before a lightning quick spell effect [pun intended]. You're dodging an acid fastball mid flight or dodging the splatter off of the primary target if you're secondary. Predicting that splatter vector can't possibly be inferred from the body mechanics of the thrower. You're dodging based on real time movement of the acid in air. It's not "that kind of" instantaneous. Nothing in the rule books says that instantaneous spells can't effectively be countered by reactions. If someone wants to waste a high level spell, they could certainly ready telekinesis to grab any thrown weapons and send them back at the attacker, and it would work on acid splash. There's no mechanical reason or logical reason it couldn't.
HOWEVER, the text of thunder step DOES indicate you can't run from the thunder. Crawford et. al. use wording like "immediately after you disappear" to indicate that there's no time to stuff a reaction between two connected events, and they both must resolve before a reaction does. If you ready the action of fleeing to trigger on a character disappearing, then someone casts thunder step, when they disappear, your goose is already cooked, because you can't outrun thunder let alone out-crawl it. Thunder damage resolves before you could even make it 5ft. After that resolves, you can flee if you still want to use your reaction. This doesn't affect the topic question though. That revolves around the order of disappearing, reappearing and thunder and not any sort of external reaction.
What's even more baffling to me is how Maxperson recognizes that the best explanation for teleportation is going through another plane/dimension but doesn't see it as 2 steps of going from the prime material plane to another realm then returning [but to a different location]; while Lyxen said it doesn't go through another plane but is two steps. If you don't go through another plane, it could work like a wormhole that is one step. If it does, there's two directions of travel. Both seem to be arguing backwards to me.
Teleportation should be 2 steps because it's double inter-planar travel even if the time in another realm is exceedingly short. As I've already said, the term instantaneous does not mean that that reappearance and disappearance happen at the same time. The fact that it says that the thunder happens right after disappearance rather than right after teleportation supports this two-step interpretation. The order of events must be disappearance, origin of thunder clap, reappearance. Note that I said "origin" of thunder and not resolution.
Here's the twist that allows player/DM interpretation. Since nothing is truly instantaneous in the sense that it takes 0 time to complete, it's possible for the caster to take damage if traveling less than 10' depending on the speeds of the steps. If the thunder clap moves so fast that it passes by the target location before reappearance, there is no damage regardless of destination. If the teleportation happens so fast that reappearance happens before the sound waves pass by, they do damage the caster if (s)he targets within 10' of the origin. The official RAW as mentioned by someone early in the topic from Xanathar is that the caster clarifies and would presumably not take damage. It would be a very minor use of rule 0 for a DM to override that especially if they let it work on the fly and then change interpretation for future use. This shouldn't have been such a long argument. The inconsistency on both sides blew my mind and might be part of why it went so long.
I'm confused at how Maxperson was right that you can't use a reaction to avoid the thunder damage but for the wrong reason. The term "instantaneous" is D&D jargon with a specific meaning not to be replaced by dictionary definitions just like words like "attack." Mechanically, instantaneous duration simply means the spell acts then is gone even if its effects continue, so those effects can't be dispelled. It has nothing to do with how fast the magic actually happens. Look at acid splash. The caster conjures a bubble of acid and physically "hurls" it at a target which can make a DEX save. It's not like pointing a finger before a lightning quick spell effect [pun intended]. You're dodging an acid fastball mid flight or dodging the splatter off of the primary target if you're secondary. Predicting that splatter vector can't possibly be inferred from the body mechanics of the thrower. You're dodging based on real time movement of the acid in air. It's not "that kind of" instantaneous. Nothing in the rule books says that instantaneous spells can't effectively be countered by reactions. If someone wants to waste a high level spell, they could certainly ready telekinesis to grab any thrown weapons and send them back at the attacker, and it would work on acid splash. There's no mechanical reason or logical reason it couldn't.
HOWEVER, the text of thunder step DOES indicate you can't run from the thunder. Crawford et. al. use wording like "immediately after you disappear" to indicate that there's no time to stuff a reaction between two connected events, and they both must resolve before a reaction does. If you ready the action of fleeing to trigger on a character disappearing, then someone casts thunder step, when they disappear, your goose is already cooked, because you can't outrun thunder let alone out-crawl it. Thunder damage resolves before you could even make it 5ft. After that resolves, you can flee if you still want to use your reaction. This doesn't affect the topic question though. That revolves around the order of disappearing, reappearing and thunder and not any sort of external reaction.
What's even more baffling to me is how Maxperson recognizes that the best explanation for teleportation is going through another plane/dimension but doesn't see it as 2 steps of going from the prime material plane to another realm then returning [but to a different location]; while Lyxen said it doesn't go through another plane but is two steps. If you don't go through another plane, it could work like a wormhole that is one step. If it does, there's two directions of travel. Both seem to be arguing backwards to me.
Teleportation should be 2 steps because it's double inter-planar travel even if the time in another realm is exceedingly short. As I've already said, the term instantaneous does not mean that that reappearance and disappearance happen at the same time. The fact that it says that the thunder happens right after disappearance rather than right after teleportation supports this two-step interpretation. The order of events must be disappearance, origin of thunder clap, reappearance. Note that I said "origin" of thunder and not resolution.
Here's the twist that allows player/DM interpretation. Since nothing is truly instantaneous in the sense that it takes 0 time to complete, it's possible for the caster to take damage if traveling less than 10' depending on the speeds of the steps. If the thunder clap moves so fast that it passes by the target location before reappearance, there is no damage regardless of destination. If the teleportation happens so fast that reappearance happens before the sound waves pass by, they do damage the caster if (s)he targets within 10' of the origin. The official RAW as mentioned by someone early in the topic from Xanathar is that the caster clarifies and would presumably not take damage. It would be a very minor use of rule 0 for a DM to override that especially if they let it work on the fly and then change interpretation for future use. This shouldn't have been such a long argument. The inconsistency on both sides blew my mind and might be part of why it went so long.