Fix some issues with New/Old config, especially for run-3 setups

There are inconsistencies with the existing configuration and run-3 layouts, e.g.

DetFlags geometry CSC False
DetFlags detdescr CSC True
MuonGeometryFlags hasCSC False

So this is a first step in trying to handle this. Firstly, I reverted the change introduced by !41271 (merged) where the MuonRecFlags were being set by MuonGeometryFlags, because these are called before auto-configuration has completed. Then, to make everything clearer MuonGeometryFlags defaults should match DetDescr defaults.

Finally, to work around the current mismatch, add a workaround to OldFlags2NewFlags to override the new ConfigFlags to match the MuonGeometryFlag version (which is correct for run-3).

I ran one of the failing tests (https://gitlab.cern.ch/atlas/athena/blob/master/MuonSpectrometer/MuonValidation/MuonRecValidation/MuonRecRTT/test/test_muonrec_Run3_asymmetric.sh#L22) which still fails, but for a different reason. ;-)

I've also run RunTier0Tests locally and see ERROR Your tag breaks the frozen tier0 policy in test q221. See run_q221/diff-root-q221.ESD.log file for more information.

which is definitely not expected. So keeping this as Draft until I can investigate.