Avoid potentially attempting to alter flags within OverlayMainContentCfg function

If inconsistent geometryVersion values are used on the command-line and in the presampled RDO file (particularly in FastChain where there is no geometryVersion in the other input file as it is an EVNT file), then it is possible that the configuration will attempt to modify flags.GeoModel.AtlasVersion after it has been locked. This merge request moves the metadata checks out of the OverlayMainContentCfg function to locations before the flags are locked.

This opens up another question about what should be done if inconsistent command-line and input file metadata are found this will be tackled in a follow-up MR.

Tagging @tadej