Thanks :)
As this was a jam, I didn't attempt to create a perfect algorithm to determine the optimal solution, but I did figure out an optimization rule that helped me design the levels. In groups of 4 pixels that could be flipped together by the previous scale, it would be "economic" to flip them together if most of them need flipping, I.E. 3 or more.
Anyways, it is possible that I made a mistake and some of the levels could be solved using less pixels, (and in fact, one level intentionally wastes pixels), but because the game requires specific amounts of yellow pixels per scale, that would not count as a level solution.
Please send me / post a screenshot if you do find an extra optimal solution.
p.s. Later in development I did consider counting the pixels together instead of per-scale, to make it always about optimization, but wasn't sure about the change and didn't have enough time anyways.