testHLT_MT.py: Fix auto-configuration for isOnline mode

The fully fledged AutoConfiguration is not usable with isOnline=True outside of P1 because it actually tries to access information from IS servers. Revert back to using AthFile directly as it was done in runHLT_standalone.py. This uncovered also a bug in that we were using an out-dated geometry/conditions tags when running on data.

The default is still isOnline=False but added a command line option to switch the mode for ease of debugging problems we are currently seeing. Once those are fixed we should set the default to isOnline=True.