If its one thing I have learned about software development, its that you must account for people doing completely non sensical things.

I knew a guy who had MS word 97, 2000, 03, and 07 all installed on the same machine, and he used all of them for various tasks. Insane? Most certainly, but welcome to humanity.

AppFS has no problem with that. The problem comes from keeping different packages on different disks -- since it caches them all into the same directory by default. It would be trivial to make it cache files from certain packages into different places as part of the configuration -- that's easy enough. The issues come into place for files that are shared (having the same SHA1) between packages, then you either have to duplicate the file or have some policy of searching for it.

A better approach, if you care about this, is simply to have a lifecycle policy where more recently used blocks live on the SSD and less recently used blocks move to slower storage (bcache can do this for you), or are deleted (this is a planned feature: http://appfs.rkeene.org/web/tktview?name=930821d0fb ).

>but it doesn't really make any sense either.

I don't need every program on my SSD. Makes perfect sense.

Aside from the obvious missing feature, there isn't even enough information to very your claims. Can I really have two versions of, say Krita, installed? Can I make a copy of that to take to an offline PC?

Yes. Since there's no explicit install step you can run as many versions as you want. You can of course copy the files to the cache of any system.