It is lighting related as the livery editor has a light source and the whole area isn’t lit up, usually it’s the right hand side that’s darker than the left
the layers should never disappear unless you set it to do that some of the colours u set in the livery editor don’t always come out that shade when on routes (different lighting related I believe) and the livery editor also has shadows which darken some parts but that’s only when in the editor (usually right side is darker than left) anything other than that is probably a quirk (bug) of that loco such as the 395 has a projecting front portion and it is possible this loco u are using could have a quirk (bug) I have not looked into it specifically
Yeah depends on your system you play on. You could try YouTube a video to try get a indication of the experience you would get.