I would not use the roofing rubber. Too many reason to list. If you really want some sort of plastic barrier I think there are better choices. Vinyl flooring or any of the sheet plastics I think are better choices. If you really want a membrane I would use one made for showers, not roofs.
Biggest concern with any sort of plastic layer over wood is making sure not to allow moisture inbetween the plastic and the wood.
Lastly, if you use any sort of plastic on the floor and first few inches of the cage walls then it really does not matter a whole lot what you use on the walls and ceilings. I say this assuming the application fits the typical reptile cage setup and won't have waterfalls, misting systems, etc.
There are some newer paints on the market that are expensive but fit all of your other criteria. Sherwin Williams Duration to name one. If you want a solid color these are a good choice. They are scrubbable in the matte finish but you are still best going with the highest gloss look you can tolerate in your cage.
If I have one issue with these it's that they approach the cost of 100% epoxy resins on a per volume basis. The paint can be applied thinner so it ends up being cheaper overall than the epoxy, but you still have to decide at what point are you willing to spend a bit more and get that much of a better finish.
Lastly, the specific question it your post title has not been addressed. To ask what paint is the safest is a bit open ended. One way to look at that question is what paints are safe during the application and curing stage. Another way is what paints are safest once cured. I would argue there is a tradeoff here. Some of the products that are most toxic during application and curing are actually the most safe once cured. And vice versa. Not exclusively true, but it is a very intractable question.
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Currently keeping:
6.10 Gonyosoma oxycephala (Javan, mixed colors)
1.1 Philodryas baroni
1.0 Rhodesian Ridgeback
