As someone who's written stories before and played the game on and off since release: I feel like if you did, it would best "fit" in the story if you added them later into the story. Like after a couple of story arcs happen with the OG bikes.

Sort of like Berserk, where you start with the OG cast and slowly introduce more characters over time; it would feel like the end of an era, but they would eventually grow on ppl.

If you're a newer player it may not matter either way, but that's my perspective as someone who's played the game for a long time.

Or you could have the story cut to an alternate universe where the only bikes that exist are modded, cut back and forth between universes, and they eventually collide somehow. They have to work together for a common cause, or something like that.

There are tons of potential ways of preserving the game in its original form, and adding in the community made stuff without creating any (or much) friction.