I think part of the problem is that Calibre should be looked at as a black box. You should not be manually fiddling with the folder structure, but using the interface. If you move/rename any books in the folders manually the database and fodlers will be out of sync. Calibre doesn't actually monitor the folder for changes, it assumes the database is correct.
It appears that Mendeley and Calibre have different user bases and were designed to do different things, it's unlike that Calibre will change significantly enough to do what you want. Of course, I'm not a developer so this is just my opinion
It seems that you will either need to keep copies of the books in both systems or use Mendeley for your academic docs and Calibre for everything else.
Of course, the brain pool might be able to come up with another way to handle it if you ask nicely and offer up the right bribes (beer generally works well)
