you can do it now (mostly)! i just finished re-organizing my entire audio library with over 250000 files (including many .pdf, .cue, .log, .jpg, etc). it takes some setting up but once done it works great
there is a new tool in Rename, Move, Copy. it is a checkbox called "move all files in folder (including non-imported files)".....but the kicker is the files MUST be non-imported for it to work
i set up a new library (not necessary but this way i wasn't messing with my old library) and chose import settings for the audio folders that ONLY import audio (minus .CUE!) and nothing else. MAKE SURE you check the "ignore files previously removed from library" box!
i made an extremely simple audio only view that ONLY shows audio files (minus CUE!)
make a smartlist. go to imort/export settings and type
[Filename (path)]="[i]file path[/i]" ~d=a ~sort=[File Type],[Filename (path)],[Filename],[Media Type],[Album Artist (auto)],[Album],[Disc #],[Track #]
what this shows you, is every file thats ever been imported into MC (from your file path), including all the non-audio stuff. Now, configure the smartlist view so you have "file type" column, and use the "file type" column to organize the view. find all the non-audio files (.jpg, .cue, .log, etc.) and delete them (from library, NOT disk!)
now, re-run the auto import with your new settings (i.e. not importing anything BUT audio minus .cue), and check the smartlist you made again to make sure you don't have any more non-audio files imported. it should just show the audio tracks now....so you're ready to move stuff!
now go to the audio only view that you created, select the files you want, and go to the rename/move/copy tool and set everything how you want it, and MAKE SURE you check the box "move all files in folder (including non imported files)". when you run the tool, ALL of the files will move that are in that folder!
after this, i went back into my old library (again, this was an unnecessary step but made me feel better) and reconfigured my import settings to: my main audio library i set to import EVERY single type of file. my "incoming folder" i set to ONLY import audio (minus CUE). I then made a few views in audio...some of them show ONLY audio (for browsing music) and some show ALL files in the folder (so i can see the .pdf, .jpg, etc). Now when i rip new stuff into the incoming, i can rename/move/copy very easily and it moves ALL the files including ALL the non-audio, but when it gets where it's going, i can use the view structure to see all the files in there.
sorry if that was long, and if you need a hand let me know. like i said i just completely re-did my entire, fairly large audio library and it didn't take any time at all and there were no real issues. ALWAYS test on a small batch of files first so you understand what is happening.
i should note also: i don't ever use theatre view, so i haven't tested it there but it should work the same (just configure the view scheme that you want)