A. The AGPM console can manage multi-domain and even multi-forest environments, and can compare any GPO it manages. So yes, AGPM can compare GPOs across different domains.

Even if you have separate AGPM instances, you can export the GPOs from one domain into a CAB file using the new export/import functionality added in AGPM 4.0, copy the CAB to the other AGPM instance, then import the GPOs from the CAB file and compare.