The current brush system has just outgrown the userbase. It was originally written over 2 years ago when nobody had any plan for the program or any idea it even existed. The way it works wasn't really 'designed' to work that way, that's just an artifact of what we did write. I knew at the time it wasn't very useful with a non-255 alpha value, but I also knew that the fix was very involved and couldn't be done in the short time that was available.
It will be improved in a future release. I have done some prototyping and a lot of thinking about how this needs to work.