You can turbocharge absolutely any engine. Engine compression can be lowered with a change of pistons and a few other changes to get it dialed in with boost. If anything, you should have two engine upgrade paths that you can follow, because they require different builds. One would be a naturally aspirated engine build, and the other would be for engines that are boost reliant. That way you would be allowed to add more boost (until you need to upgrade your turbo system) as you upgrade your engine to handle it. Some engines will be better off being built one way or the other, just like in real life.
Besides, has anyone else actually looked at the boost gauge in both this and previous GT games? Something tells me a stock Daihatsu engine can't handle that much pressure...
As for room, they make rear mount turbo kits which take up very little room (if any) in the engine bay. You can also relocate the battery, perform an AC delete, etc. to free up more space. The aftermarket bolt-on kits are designed to work with an otherwise stock vehicle with very few changes. An afternoon's worth of effort will allow for plenty of room in most engine bays.
In addition, you don't need an available bolt-on vehicle-specific kit for a turbo to work. They sell compressors. They sell intercoolers. They sell BOV's. They sell piping. They sell oil lines. Very few people I know buy the actual kit for their vehicle; they usually just piece them together based on what they have to work with. If they spent a little time freeing up their engine bay, they're usually able to route the pipe better than what's available in the kit.
Superchargers are a different story though lol