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Yes, regular session files (*.qtr) only store file references so that if you save it to another filename (Save As...) ALL file references will still point to the very same file locations, although in relative paths to the session directory, whatever it is at the moment you execute the save operation.

Note that the said "session directory" is about the place where new media files (audio or MIDI) will be created and stored on recording at a given moment--it doesn't mean at all that any files used by that session are in the same place or directory--again, only new created and/or recorded material will be stored there.
Yes it's true, you can set the session directory to any, even the same, directory or folder, all the time, for all sessions. You may find it ludicrous but it's how qtractor works since its conception, and pardon me, it won't change any day soon if ever. Sorry.

However, there's one particular exception to this scenario, one you ought to try and use whenever you wish to move away and/or rename the session directory in a self-contained format: the session archive/zip bundle (*.qtz): just rename the session file suffix (extension) from ".qtr" to ".qtz" in the File > Save As... dialog and you'll see what it gives ;)

hth.
cheers

cheers