I do think most of these things are intended behavior.
But, hmm, yeah I do see what you mean about the palette turning gray in the "Stroke..." menu while transparency mask is active... That's confusing.
I hadn't noticed that because I tend to use the Toolbars.
(Found in the menu bar under Decker > Toolbars)
This is with transparency mask on -- the background transparent white has turned gray but the sidebar palette white (which is now opaque) still looks white.
But yeah, I see what you mean about it being weird when you're working directly from the menu bars at the top.
For the other stuff, the difference between the two black colors isn't relevant very often. For most users, I think just using '1' all the time is fine.
For '0' and '32' however... it generally makes sense to me that you can only draw with opaque white while transparency mask is active because it's also one of the only times when you can see the difference between the two whites. And I tend to think of this use of the word mask not as in "thing you look through" but as in "thing that masks off areas of white" like masking fluid in watercolor painting, but that might just be my own association with it.
Anyway I wonder if the toolbars would be helpful to you for now? It doesn't answer all of the things you mentioned but it does sidestep one issue (and I think they're very useful in general while drawing in Decker).