I personally think that Undertale as the finale was a stroke of genius which should prove to be very lucrative for the charity.
I can see them getting more money with WWHD > SM > UT than UT > SM > WWHD simply by having 2.5 hours more to rack up Save the Animals vs. Save the Frames donations. :V And there's probably going to be a lot of appeal to closing with an immensely popular game that has never been seen at a GDQ before.
But it's gonna go under 90 minutes, because these kinds of runs always beat their times, and maybe this is just me, but that takes a lot away from the tension and the viewership investment. If something goes wrong, then that sucks, but it's not nearly as soul-crushing screwing up 80 minutes into a game as screwing up 210 minutes into a game. I don't give two damns about Final Fantasy 6 but the SDGQ 2016 run of it was incredibly nerve-wracking for exactly this reason.
I'm hoping to be wrong about this in the end, and I'm sure the show is going to be fantastic no matter what they do (they could have ended with Cheetahmen and still done great), but I can't help being cautiously pessimistic about it. I dunno. Maybe I'm concerned about nothing.