Heyo Again xD Hmm out of curiosity which version of color swap do you currently have? Selection of cels was added in 1.1.0 which should have the functionality your mentioning! (1.1.1 is currently the most up to date though too) but yee just need to check the checkbox option to swap / export selected cels. This should only select the currently selected cels instead of everything on the layers.
This short shows the cel selection stuff! Though if its not this let me know if im misunderstanding ha Let me know either way though because it should be working haha :)
On the undos I def get that xD Technically each color swap is doing a bunch behind the scenes in a single undo action. It might be possible to add an undo button to the ui which would pull back the last group of swaps but not sure if it could tie in to the ctrl + z compleatly but yeah might be able to figured something out to make that less of a pain!
Also thank you for taking the time to provide all your feedback and your lengthy messages :) and yeeeeee thank you for spreading the word!!