More of an update. The LX200R is really just the optical tube. The base is just a LX200GPS. Playing with it a few more nights I've found the following:

• Sync and Slews give the correct coordinates to the mount. The mount is really at those coordinates
• The position that indi/ekos/kstars thinks the mount get an offset. This varies from 10' to 35' in both RA and DEC. So if I do a sync it syncs the telescope correct (as in the telescope itself on the handpad shows it correct), however the position in indi/ekos/kstars automatically jumps back off.