Oh, I have absolutely no problem with states requesting their equipment be painted in custom liveries. In fact, I think it's a good thing, especially since Amtrak is no longer financially contributing to these services. A unique brand makes it clear that the state-supported services are different than the national network. (It also makes it easier for the states to "divorce" Amtrak in the future.)
My gripe is about things like the brand new California Venture trainsets not matching the nearly new California Charger locomotives. It's sloppy... but that's on Caltrans and Siemens.
But even more egregious is Amtrak's intentional hodgepodge of Phase V locomotives, Phase III Viewliner II cars, and the Phase VI Superliner/Viewliner I cars used on the National Network. It looks extremely sloppy. If Amtrak can't figure out something simple, like how to paint the trains, it speaks volumes about how disorganized the company is.