..Yes, of course, everything written below can be done in photoshop, but...
It would be nice to have alpha mask editor built in Autopano. When adding photos to panorama we can select a photo end draw over it a invisibility mask with simple tool - box, circle and ofcourse brush tool.
More.. it could be useful when we can copy mask from one photo to another (many).
With this enhancement using photoshop and saving as png24+alpha will be unnecessary.
We had last week the devplan meeting for autopano v3. The main feature is the masking tool integration. But there will be also some other new feature. I will post some proposal soon in the forum so you can vote for the small feature.