Wow, that's quite the (both) useable and useful software - thank you for the link. I'm not normally part of the "x should buy this out" group, but in this case, Amazon really should.
No, they shouldn't - because if it goes against their business interest (having Amazon-bought books look better than manually uploaded content), they'll shut the project down.
The only reason this software is any good is specifically because it isn't controlled by Amazon. This functionality is very deliberately missing from the stock Kindle.