Hi Chris
I have the EXACT same problem - same projection and everything (GDA94 MGA Zone 55). However, I do have GCPs. When I export ortho-photos, it appears to put them into the WGS84 Geographic Coordinate system in decimal degrees (not projected coordinate system in metres). I too want to open the files in Global Mapper and do processing before exporting to GIS.
Did you end up resolving this issue with RC - i.e. did you figure out how to export in GDA94 MGA Zone 55?
Cheers
Reece