I once found a gameshark code that was corrupt and put a master ball in my key items pocket. This master ball worked just fine and could be used over and over. So, there may be a chance that if you registered TMs in the Key Items pocket that it might work. I know it would look weird but it's worth a shot.
I'm sure that there is a code somewhere that determines the difference between a disposable and reusable item, and if the could be changed, it would would have a much nicer look to it.