The flashing masks come from the fact that the renpy engine desyncs the actual animation and the mask animation. In renpy to play a movie with a transparency mask you need to overlay two movies (the actual one and the mask). It usually works fine but if something desyncs it goes haywire. I have been fighting this almost since the beginning with multiple iterations of trying to optimize, preload, etc them. I didn't want to use pure images for animations since those took several times more space than a movie but I might have to return to this approach. With the conversion to webp the images are much smaller, so the overhead will be lower for the added benefit of the animation stability.
As for the rest I will take it under consideration. I am still experimenting with a lot of ideas so nothing is off the table.