I'm sure it would be fine proceeding in that way but, ideally, you need to get 3-4 layers of the heavier CSM on at the same time so that the build-up of the tooling resin can reach its usual curing temperature. Less resin applied would likely lead to patches similar to what you've seen rather than limit them

I wouldn't worry at all regarding the slightly different colour of the cured resin, as long as your surface gel coat is sound and everything has cured hard

I've seen similar patches many times on different moulds and as Hanaldo said, it's likely that some patches cured at slightly different temperatures or that some parts of the resin were richer in the filler element of the product which you can sometimes see accumulated at the bottom of the can if not thoroughly mixed before use