Yeah, 1:28 is too small. It's not that it wouldn't look okay with the truck - it's that Alts wouldn't fit into it.
I've measured the toy again and did some calculations for a 1:24 scale Peterbilt, and Optimus would have to be exactly one inch longer in truck mode to be in perfect scale with Alts. As it is, he's 1:26, which is pretty well close enough, all things considered. I doubt Hasbro will make another version of movie Prime that's 8% larger just for finicky sticklers like myself, so I'll take it

As for repainting Prime himself, I think it's a bit early to do that. He's a movie toy, so he'll probably get a G1 redeco, and he's a Prime toy, so he'll probably get a Magnus or Nemesis redeco... he's a long-nose cab, so he could get a
G2 deco... the list goes on. I'm content to wait and see before I break out the airbrush for the cab.