If you want to give it a shot but get annoyed by the fighting system, try it as a social character, zero-fight gameplays are possible.
I can do play the game just fine but I end up missing a lot because I can't tell if from rocks.
I couldn't find anything similar for Linux distros, though.
Edit: thinking about it more, the easiest way to get something like this would be to just put an overlay on my monitor with the coating that the enchroma uses. This would pretty much solve my issues.
These days I use Enchroma [0] glasses. I still can't identify colors that well, but it helps with differentiation.
EDIT: It seems in this case it would have to go further than BG2, but I stand by the claim that BG2 style highlighting is a useful accessibility/convenience feature, and I personally did not find it immersion-breaking.
It also makes exploring more efficient, as you can search containers and interact with objects and characters a quasi 3D world without the need for 3D rotation. Which I think is important for the kind of game Fallout is.
There's really no way to make a more atmospheric game with that engine than FOT itself.