I agree that ZEUS shadowing/lightening are kinda weird, but it is what made the game to look great.Even reviews that did not like the gameplay back in 1997, praised the graphics - that could be easily checked also on alt.google.groups
However, I do believe we are not talking about those effects only, as whole layers might be missing:
Please, notice the grid in the background. I'm sure you will agree it is not only brightening difference.
I can also check if YourMKArcadeSource can provide more clear screenshots if you want, as I saw people think the video quality capture was bad. He has already contributed with several rare MK roms and said to ping him, in case of any assistance, as he would be more than happy to help.