Each database in sync stores is an independent container, therefore this can’t be avoided. One workaround is to use smart rules to move the items immediately to the desired database or to use a less frequent sync schedule (e.g. hourly).
You could simply not sync the Global Inbox. Meaning you use for the Mac and for the mobile device(s) two seperate interim locations where you import all the items before you have them sorted.
One of these interim locations could be the Global Inbox, of course. Say, you use it on your Mac and have Smart Rules move the files (or you sort them manually).
On the mobile device you could sort items manually to their final location and only have that database(s) synced. Sorting on a mobile device is not that comfortable as you know—no Smart Rules but manual labour is necessary. Depending on the number of them that could be cumbersome.
When you use for mobile another interim location instead, say, the inbox of a database which gets synced, you could again leave the sorting to Smart Rules on the Mac. This would increase the data upload over syncing after manual sorting but only in one direction, mobile to Mac.