Great news, I've figured out how to do this in PkHex:
It looks like all you need to do is go to the Block Data menu in the SAV tab of PkHex, then scroll down (about halfway )to NationalDex and change its value from False to True. This will check off your "Received National Dex" Event Flag and set the Event Constant for National Dex Enabled to 770, which would confirm that they only change after the National Dex is obtained, and do not give it to you by themselves.
I haven't played FLRG so I cannot verify whether that allows you to trade with them, but this procedure works to give a new save the National Dex, provided that save has the Hoenn Dex already.
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