I'm not able to answer your question on the intimate details of matching on the device, i haven't looked at that code.
I can tell you that all this plugin does is a search for ondevice:true at the time it does a sync, so the same as the tick marks you see in the gui.
As for forcing a book back onto your device that you have modified, yes the usual send to device will work. I mentioned in an earlier post that such a case would become a problem for this plugin by only syncing the differences to a list. The only potential solution from a plugin perspective I could think of was an option for a list to always sync the entire list. So you could create an "Edited" list for instance with this option on that always gets synced. If people think that would be useful I will add it.