1) Why take fighter at first level? The rationale explained in the OP doesn't seem to hold water for me.
Con saves are great, but a proficiency in strength saves is completely useless for almost every version of this build except the fighter/rogue/pally version. Additionally, strength based saves aren't super important or common in most situations. Going with rogue to level 3 for archetype selection as early as possible seems to make more sense as it gets you the ability to autocrit unaware enemies for surprise round nova at level 3. Going rogue to level 4 before dipping fighter would let you choose a feat. Alert will make your surprise round more productive by ensuring you go first, but you could also take the resilient feat and to get a +1 in con and proficiency on con saves. For the build I'm trying to create, dex saves are going to be more frequent and important than con saves for levels 4-6. At either level 4 or 8, the resilient (con) feat will get you the con save proficiency at a point where it starts to matter more during gameplay. The whole point here is that I want to understand if fighter really is the best option at level one for my build concept. Even though I'd need to take a feat to get it, by level 8 I will have proficiency in all of the saves that are most relevant to the build (except wisdom).
2) Why all the love for charisma and deception?
Is there some game mechanic that I am missing which provides a good reason for this? Deception in combat isn't addressed in the PHB, so it's not like you can feint in battle to get advantage by RAW that I know of. By RAW, the feint combat maneuver of a battle master is keyed off of dex (or str, but that wouldn't make sense in this build) so cha is no real benefit there. Perhaps the DMG or other sources mention something I'm not aware of? Outside of combat, I could see how it could lead to catching more opponents unaware during the first round of combat by approaching as if you were going to parley and then just attacking. However, initiating combat from stealth nets the same effect without the need for pumping charisma or the chance that intelligent foes who have heard of your deceptive tactics will get advantage to oppose your deception rolls because you have become notorious for this behavior. For the build I'm after, it seems like I could either dump cha to 8, or leave it at 10 and put the other points in to wis and int. This would get me better passive and active perception, insight and investigation.
1. Bare in mind this is just a guide to help others get their feet under them, and not necessarily the end-all be-all of Rogue Assassin builds. I think it is great that you have a specific build and feel in mind for yours, and even greater that you feel it should differ in some aspects from the presented build.
This guide is set up to present Assassin's with the highest survivability and maximum Assassinate nova.
I believe as well, reading through the guide, the premise is to set up the higher HP and sought after Con proficiency first. Get the Assassin sub-class of the build's namesake, and then finish off towards that extra attack. As the build states, that is around lvl 8 if the guide is followed.
The strength based saves are not a highly sought object in the build. It assumes that you are building Dex, to still have an okay save, while ensuring the Con save, which generally guards against nasty effects, instead of pure damage is built up as well. (The higher HD and assumed high dex score is meant to mitigate the typical damage centric Dex checks)
The build specifically points out Alert as a choice feat. Which is something that one can pick up if using feats and the variant Human racials also suggested in the guide.
Your final question in this segment is really up to you. Do YOU think that going fighter is the best option for your concept. This is what the OP's opinion is from according to his/her stated objectives. Only you can answer whether it works for you or not.
2. The mechanic in question isn't so much a matter of crunch but role play and being able to walk up to an intended assassination target and surprise them. Deceptions and disguise is how that is accomplished. Typically. Perhaps your table does things differently. The thought is that not all assassinations occur from an ambush on a forested road or isolated room. They can be equally in well guarded areas or crowded city plazas. This is more where being able to get close to your target undetected where purely being unseen is not possible. What's more, they can be useful stills for information gathering on the target so that you can learn when she likes to use the out of the way privy or where he enjoys long horse rides, with a minimal contingent of guards.
Otherwise... just being an in-combat assassin feels... less. Not making judgement on those that prefer that play style. I just understand and appreciate the ability of a good assassin to be able to smile and chat with their target and then the next day stab them in the gut at their weakest.
If you feel your build isn't served in this manner, forget it, and reallocate your ability scores accordingly. That is a matter of vision and play style, not the right or wrong way to build an assassin.