I highly doubt the game uses 16 bit color mode. I'll look at that scene again, but it's probably just a color banding due to transparency overlays. All their games so far (MGS2, ZOE2) used 24bit color mode, and I didn't see any dithering on the clouds. at the beginning of the intro, where it would be bound to appear had it been rendered at 16bit.
Btw, you can always zoom into the cutscene using the triangle key. Whenever you are in doubt if it's a video or raltime

Also, in the parts of the cutscene where it allows you to switch the perspective with R1, you can also move the view around with the left stick while holding the R1.