The ability to change the channel layout on each layer in every scene has been, for me, one of the huge killer features for the SQs over other desks. I love watching the faces of X32/M32 guys as I completely change out fader layers at each scene to keep only the channels I need under my fingers without having to do any oddball abusing of DCAs. 
Having said that, there are contexts in which it would be handy to have only some of the layers change and not all of them — at the moment, it’s all-or-nothing. If I have one layer that shouldn’t ever change and I need to update it, I now have to load up every individual scene, make that change, and then save the scene, which is painful and error-prone.
It would be ideal to have the “Strip Assign” filter broken into the individual layers, so you could safe a particular layer and not-safe others. As a minimal option, it’d work for me at least to just have a “frozen layer” checkbox somewhere that tags one pre-determined layer as permanently safed from changes regardless of the status of the “Strip Assign” safe. (So, check that box and however layer A is set will never change between scenes.)