I might be wrong but skybox issue might be due to lack of other blending modes for transparent textures on the PC version. PC version can only do additive blending, while PSX has 4 blending modes. In TR4/TRLE if you use a FLEP patch you can restore other blending modes (5 in total) and it changes how some particle effects look.
The lighting differences are interesting. I know that there is a significant difference in lighting between PC and PSX due to DirectX 5. For example TR3 lighting is very bland and washed out on PC because of older DirectX version limitation. You could try playing Chronicles in software mode to see if there's any difference. The lighting should be more saturated.
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