Most professional image-editing tools provide the feature which allows the user to select which channels are visible (R, G, B and/or alpha) and which of them are being edited. On first sight this looks like an advanced option, but actually some part of it really isn't that far-fetched and it often comes in handy.
I'd like to propose a subset of this functionality to be added to Paintbrush:
The requested feature would only give the possibility to edit the alpha-channel separately. This would come down to adding a mode in which the user can edit the alpha-channel in grayscale mode, with the grayscale-level representing the alpha-value.
On a side note: is there any reason why transparent areas are simply put in grey, instead of the more common "checkerboard" pattern?