I just implemented selectable display layers. There's still a few quirks to work out but hopefully they're pretty minor.

Here are a few screenshots:

Some layers need to be added, there should be some options for making the 'low contrast' display layers have a custom alpha channel, the top icon should do something (like toggle all or the selected bits), there's a deeper issue with the module text fields not being associated with any layer (that's why the blue "CR..." text is so visible) which needs to be dealt with, and the vias look to inherit whatever trace they are associated with (which is probably a deeper issue with the vias) but other than that it's working!

I decided to push this 'good enough' solution so that the basic functionality is there and I can try to add and extend to it later.