So, are Indy 2 and 3 confirmed to be the same master as the DVD and HDTV? I've read somewhere that they come from a new 4K scan as well, only they didn't get the same level of restoration as ROTLA but that info could of course be wrong.

And actually the possibility of the ROTLA print being a new one didn't even occur to me. Did they make 35mm prints from the new master? I thought it was just IMAX and digital?

Anyway, I think jero32 got it right - going from the negative, they'd have to do a new colour timing and trust me, I know that digitally emulating photochemical colour timing is very hard, so they probably did the timing based on some non-fade source but it looks a bit different due to it being done digitally. From what I know about the way such restoration process normally works, it's more than likely that that is the case for most BDs. Unlike on LD and DVD masters, where they usually probably just tried to compensate for whatever fading there was on the film source they used.