You're right that there seem to be interaction rules that are not stated in the tips. If you play a long game, then new pixels added later in the game are wiped out easily.
Having recently done some agent-based modeling work which is related to automata (even though in this case non-deterministic), I wanted to try out how few pixels I could add from the pseudo god mode to turn the tide in different situations. And, as you noted, late in a single game, established colors have some sort of implicit advantage with much higher numbers, regardless of how many new pixels you add.
I also agree with you that the interface adds to the frustration. It takes a long time to place pixels, when I imagine the interesting part for most people is the result of different placements, not the challenge of getting the pixels into place.