Thanks for playing it all the way through, and for both notes.
The upgrade menu one is fixed in 0.5.0: the tree now slides under the title bar and the outline when you drag it.
You are right about the phishing mail. Nothing stops one from appearing right under the pointer, and getting locked by something you had no chance to see is not fair. It is not in 0.5.0, but it is on the list for the next update.