You're right in thinking that most of those side quests are primarily done at the end of the game or for post-game. You can get the fossil Pokémon you didn't choose as soon as you get to Fuchsia City, though.
The sidequests are all thrown in to let you get most of the remaining Pokémon not obtainable through other means. My goal with this hack is to make the native FireRed into the most option-diverse (through nostalgic inclusions or otherwise) and convenient game it can be while keeping it essentially the same game. If you can get all the Pokémon in the game in credible, semi-authentic ways and get the feeling that the game has become less of a hassle to play (and has more options), then I'd say this hack is fulfilling it's job.
The hack is completely fulfilling it's job then! :D
I've now been through every gym, going for E4 atm. I got the second fossil pokemon and the bulbasaur too!
I'm wondering, the extras in the first post (bug catcher, route 10 pokecenter, ...) - you state them as significant in game. How so? In most of them I can't even identify the differences. Are they side-quests too in some way? What do you mean by significant?