In my (quite considerable) experience with a wide variety of non-core extensions I have seen them all over the place and with total disregard to any "standard" document, assumed or otherwise.
We have
/cache/etc....
/media/etc...
/tmp/etc...
/components/com_whatever/etc...
/templates/template_whatever/etc
The only one of the above that can be "flushed" from Joomla admin is the cache folder therefore if you want Joomla Admins to be able to flush the cached items they should be in there else you would have to roll your own way to delete/flush your cached items
I dont believe there are any hard and set rules... well Joomla doesnt dictate them... maybe it should, who knows...
At the moment its a free for all - so be free! :-)