Ok so Agon prep...
Island Concept: A name & description : My assumption is used to create specific areas on the island as well as to generate consistent description throughout play.
Signs of the Gods: Select 2 or 3 gods who might have interest on the island and decide on their desires as well as what signs the would use to convey their desires. the leader of the heroes can interpret these signs as concrete actions to gain divine favor.
Design NPC's/monsters: Create 3-5 npc's and/or monsters that embody the overall concept of the island. They should want something concrete that conflicts with those who oppose them. A singular desire with 2-3 qualities. They serve as allies and opponents to the PC's
Create Strife & Trials: ( The core trouble that keeps the island in a state of woe) as well as 3-4 trials (conflicts) that address it's symptoms. This prep serves to create challenges for the PC's and lead to the climactic trial to end the Strife.
Create Mysteries: Highlight a few questions that the trials may raise for the characters that the Strife player (akin to the DM) can answer. These serve as things for the players to discover, thought the answer is a strong hypothesis for the Strife Player. Honestly I think Agon kind of drops the ball in explaining how these mysteries are resolved. on the one hand it suggests they are questions... but on the other hand no procedure for determining their answer is given, and it is implied that ultimately it is decided by the Strife player at some point during play.
Special Rewards: A unique and remarkable reward the heroes might gain from helping the people, defying the gods, overcoming challenges or uncovering mysteries. This serves as a reward, pretty self-explanatory.
So to tell you how I see commonalities in D&D prep... let's look at a basic 5 room dungeon....
Concept: The dungeon will have a general concept that serves the same purpose as that above. In latter editions of D&D the description of the individual rooms might be detailed but it could also be sparse to non-existent in the OSR style.
Signs of the Gods: This prep is unique to Agon play and unnecessary for D&D play due to it's theme... though it could be something interesting to add to D&D campaigns of a certain type. Interpret the signs of the gods and receive inspiration.
Design NPC's/monsters - In general the same purpose as D&D... allies and/or opposition. In the confined space of a 5 room dungeon you'd probably create a similar number though they'd be more detailed (stat blocks for monsters/but not necessarily for NPC's) due to different systems.
Strife and Trials: While Strife isn't something that would need to be prepped for D&D... many do in the form of the climactic battle. This ultimately serves the same purpose as combat, traps, skill challenges, hazards, etc. as D&D. Though usually at a much lower level of granularity than D&D.
Mysteries: Knowledge that the PC's don't have that must be discovered through play... both systems have this. Answer is determined by the DM/Strife player and neither are particularly specific about when the truth of these mysteries has to be determined.
Special Rewards: Exists in both systems... are determined by the DM/Strife player. Very little difference except D&D provides more examples and lists one can choose from.
I honestly don't see the prep for the two games as having this vast gulf of difference outside of their mechanics being different. I guess the island is more nebulous as far as its physicality but you're doing similar prep and just not assigning it a location in Agon... though to be fair there are methodologies in D&D where location is kept vague until actual play takes place like point crawl and random dungeons. I'd be interested to hear your take on it though.
A few things leap out at me here. I'll preface this by saying I've not yet run or played Agon, but I have read it, and I've seen it played. I backed the kickstarter and I do want to get it to my table at some point.
I would say that the biggest difference between Agon and D&D is that there is a clear structure to prep in Agon, and then the ideas within that structure are more about inspiring participants. With D&D, there structure is far less specific... many would say that there isn't one, though I don't know if I'd go quite that far... and then the ideas in that loose structure are far more specific.
Agon tells you exactly how to prep for play. And that prep is very simple and broad. Assuming you decide to make your own island instead of using one of those offered in the book, of course. It breaks it down into components (Signs of the Gods, Arrival, Trials, Characters, Places, Special Rewards, Mysteries) but the details for those components are not designed to limit players. They're also not hidden. The Strife Player reads the Signs of the Gods out loud at the start of the session, then they read the Arrival. They introduce characters and they share details such as "this person is clearly hiding something" and so on. Their job is to Reveal, and that's made very clear in the book.... Reveal, Ask, Judge is the basic loop of play.
To touch on Mysteries, I don't think it's that vague at all. They're meant to be answered in play. These are questions prompted by the characters and location... so they come about as a result of the mix of elements for a given island. It may be "why is the priest of Hera turning her back on the people?" or similar. The Strife Player is recommended to offer a partial answer, but to then let play determine the truth. The players can either confirm the hypothesis of the Strife Player, or reject it for their own. This is all stated on page 137. Then the example islands have some Mysteries, which you can see are just leading questions to determine in play.
Now, compare that to D&D. The structure of D&D is far less specific. The DM is meant to craft an adventure of some sort, which will have a Beginning, Middle, and End (this is from the DMG, Part 2, Master of Adventures). They offer some types of adventures (location-based, event-based, mysteries, framing events) and gives advice about some elements of each (party goals, villains, events, suspects, and so on). This is all very broad. So much is left to the GM to do... right down to the very basics of what the structure of play will be.
Then, the elements chosen need to be detailed. You need a map for locations, you need detailed stats for opponents or traps, you need to design encounters, and so on. There are a lot of tables you can use to determine these elements, but it's all scattershot and the guidance is super vague and wishy-washy. Mostly, prep consists of determining specifics ahead of time.
I think the two are fairly opposite in how they work.