I agree that video quality is more important than bonus features.
I haven’t looked at all the discs yet, but I think the solution should depends on how much space the bonus material takes up. If it could be 3x feature BD25s and 1x bonus disc, that sounds good to me. If it would be 3x bonus discs, I think it would be a much better decision to use 3x BD50s than have a 6-disc set.