So far you had to import all of your files into calibre, it can't reference external files. So it is pretty much unusable for importing larger existing libraries, and you get locked in.
For me, I think this is a feature.
It ensures that no matter what plugins / convertors / bugs calbre has at the time, your original files don't get mucked up. So you can merge records, mess about with meta data, and not have to worry about losing anything.
The copies that are imported into calibre's own library folder are just that: plain copies. I don't get your point about "locked in". You're as locked in as you were with your original files. The directory layout may be different, but nothing gets obfuscated.