The processing workflow for RTK should be similar to PPK. In the end, you are dealing with image datasets that have highly accurate geotags, only their origin differs.
If you are getting some shifts, I would suggest first double-checking the PPK correction process and make sure the appropriate data was chosen:
- the rover file (rinex data from the drone) - ensure there was no strong wind that induced vibrations to your drone.
- the base station file (rinex data from a fixed base station) - this should be as close to your study area as possible.
- broadcast ephemeris data (precise satellite navigation data) - this acounts for orbital errors and should be reliable.
The last resort would be to correct the shift by including GCPs in the project. RTK/PPK geotags in consumer drones is a relatively new technology and the workflows for using them have not yet been clearly defined in the industry. To what extent they can replace GCPs as a means for high accuracy in mapping is not thoroughly understood. In general, the best practices would still require the use of GCPs and checkpoints to meet proven absolute accuracy standards.
However, the benefit of RTK/PPK image geotags is that you can reduce the number of GCPs collected for a given project.
Hopefully this makes sense.