Why do you want to store mutes per pattern? It’s perfect how it works on the MD, but maybe I’m biased because I spent so much time with the MD and its design choices. When you would like to store a mute with a pattern, or kit to be precise, set the track volume to zero. You can use track volumes for mutes that are stored with a pattern and still have amp volumes for mixing. When you mute a track with a track mute, it will stay muted for sure no matter to which pattern you’re going to jump. Regarding RAM machines and CTR-AL you should better be sure that they will not accidently start playing just because you switched a pattern. I’d been using green and red stickers to mark tracks that should never be playing simultaneously (mostly RAM recorders and RAM playback machines when they both had trigs on the start of a bar).