I think I have a similar setup on one of my boxes, a “large” policy covering my whole home account, and two separate subdirectories that I want to have different policies on, and the snapshot create --all (or the equivalent for the GUI) will do all, but also notice that the dirs overlap and that (at least in my case) the files in the two smaller subdirs haven’t changed during the run, so it just builds a snapshot listing and sends over. The expiration differences are handled by the maintenance jobs, so its not a problem for the machine that it runs over the same dirs once or twice extra, that is almost “for free” on the client and just causes a bit more work on maintenance to keep track of when items expire from three lists (where one list is lots larger than the two subdirs) but that it the computer working and not me so I don’t mind that.
I think you should do several policies for the different expiration schemes.