Is there a complete and detailed description of what Migration Assistant copies over?
Migration Assistant is fairly well documented in http://support.apple.com/kb/HT4413 - basically if a newer or equivalent version of a file is not present, it gets moved by default.

In your case ~/Library is moved if you select that user - you can't deselect it like some other folders in the home folder.

Applications (which includes /Library/Application support as well as /Applications) move when that is selected.

Files in / only move if you choose other files. Everything goes AFAIK. Even ByHost preferences that no longer are used since the host has changed.