I was pulling my hair out with this app for a while. I did some playing around with it last night and confirmed that since upgrading to iTunes 11 (I actually didn't want to but it did so automatically when I upgraded to Mt. Lion), and using the last version of Podcasts (I didn't update yet), it is syncing playback position with my macbook.
Up until last night I had each podcast set on my iOS devices (iPad 3 and iPhone 5) NOT to automatically download. Then I would listen and then still sync to iTunes. It would update them via syncing, yet the app would show new episodes before I had downloaded them, I was just doing it this way.
However, last night I tried unchecking the "automatically sync . . . " and then only selected some old podcasts that I like to have on my device, so in other words it will not update my current subscriptions via the cable (I still sync for musice that I rip from CD's and photos basically, and to backup). Then I turned on automatic downloads for each current podcast I subscribe to on the two iOS devices. So we'll see how it works using the automatic downloads.
One thing is clear, if you have iOS devices set to sync subscriptions via iCloud and still sync those same podcasts with iTunes on a mac, you will have a lot of screwups. Mainly you will listen to something, it will show as unplayed, then you sync with your mac, and it will re-sync that same episode which your mac thinks you didn't listen to, and then screw up your play status.
I did verify that the playback position does sync with itunes over iCloud, HOWEVER - if you look at each episode it doesn't look like it, because it still shows as unplayed with the full circle filled on. Yet if you click on an episode that you've already started listening to on an iOS device, it will pick up where you were, but it's decieving.
Sorry for my confusing post, but this topic is confusing, and they haven't made it any better. I'm about one more screw up from downloading Downcast. What I'm trying now is to just stop syncing those podcasts between the mac and iOS devices, so I basically turned that off, however, I didn't completely uncheck to sycning "Podcasts" in iTunes because I thought I might lose some episodes. Eventually I'm going to turn it off becasue in reality I rarely ever listen on my mac.