It could be, but then fans will just ask: Why not just have Legends travel to a future or alternate Gotham with an established Batman already?
Gotham has a story that it wants to tell within its own show's boundaries, that's why it justifies itself as a prequel and whatnot. But in a crossover (especially one only told in a Legends episode, given that Gotham is ending), it can be very tempting to just focus on the weird aspects and emphasize: "Yeah, Gotham is this weird show. It just is. Now have a laugh at all these settings and characters they built up, cause you don't know the context behind them."
Like I said, I'm much more comfortable with it crossing over with the other shows not set in the CW verse.