Hello,
All these are already fixed since MatchMover 3.1 (nov 2004).
For the auto key setting, it's automatically disabled if you edit anything on the track (it turns it to manual), so you should not need to set it manually. But as you noticed, using the contextual menu is the only workaround.
The RZML export was (for v3.0) only used as a gateway to ImageModeler. So there was no real need to reimport it into MatchMover (you can still import a 3D obj from ImageModeler if needed). If you need to edit some values, you can do it through rz2 / rz3 ascii export/import.
The RZML import functionality that is now included in 3.1 is compatible with both ImageModeler and Stitcher.
Hope this helps