You're completely forgetting that there are already cars in the game right now that have had different manufacturer's engines in them. I'm talking about the same car different brand thing that is going on in real life but also in the game. The Subaru and Scion with a Toyota engine, or the Infiniti with a Nissan engine. Both have exactly the same engines but have different branding. So you can't say that manufacturer's won't agree to it. They're doing it anyway.
What about tuner cars? Hmm? They've basically done what the "hackers" are doing. A Nissan car but made better and named Nismo or a Mazda made better named RE Amemiya. Isn't this not what you're saying the manufacturer's would never agree to? I beg to differ.
There's so many manufacturer's in the game that are in partnership or are part of a greater company. So I don't see them having a problem with it. My dad's car in real life - a Nissan Note - bought from the Nissan dealer. And it has a Peugot engine . . .
If that's not an engine swap that the "manufacturer's would never agree to" then you need to reassess the automotive industry.
Nismo is
Nissan's
Motorsports section, just like TRD is Toyota Racing Development. Infinity, Scion, Lexus are all subbrands of a parent company. In this case they would be Nissan and Toyota. Toyota GT86 has a Subaru engine because it was a joint venture between two companies to reduce production cost. Yes Re Amemiya is a specialized independent tuner which improved base specs of rotaties, they do the same thing you do. The important difference between modding and included game content is LICENSING. Are people really this dense and don't see the difference?
If you want a real live comparison: If you bring your freshly purchased RX7 to Re Amemiya and have it modified, you void your warranty on the car.
As for Mod support. Games need to be fully designed around a Mod support. Skyrim has no Online aspect, there a mod support is without any negative consequences to people trying to enjoy the game in its pure state. Starcraft/Warcraft have strong modding as well, but mods don't interfere to into league matches, they have dedicated sections (DOTA). Halflife->Counterstrike same story. World of Warcraft does not have a Mod support because it would intrude the gaming experience for people. Supporting a modding community is a choice of a game producer. The mod community taking things into their own hand and intruding a community, which has no way to separate itself and prevent modders from joining pure gaming intentions, is just plain rude.
If GT6 supports modding, so be it. All that needs to be ensured is that there is a separate, dedicated server/location where this can be done. The danger and possibility that a modder interferes in undesired situations is what ruins the game for many.
Under this aspect, I hope you can see why the demand for official mod support in GT5 is a bit outrageous.
Just to clarify. I do enjoy mods myself in games that support them. Changing skins on Skyrim armor is awesome and expands the game experience. The difference there is that I dont interfere with anybody. Human common sense can not be taken for granted sadly and people will try to ruin the fun for others by exploiting.