I'm in PQC right now (actually leaving today), but I flew directly from outside Vietnam and am similarly departing.
My understanding was that a domestic flight requires clearing immigration at the point of arrival in the country. Of course, SGN-PQC would be a domestic flight.
I don't know a lot of countries where you can transit to domestic without immigration at the point of entering the country. I know Thailand is somewhat an exception, though it really isn't: your bags might be routed directly to your final destination without needing to claim them, but in the transit channel back to the relevant terminal you must clear immigration (at which point I imagine you need to present a visa if applicable). At the final destination, you are directed to a separated baggage reclaim (as if you arrived on an international flight) which is where you also pass customs.
EDIT: Interesting - just read Vietnam visa rules from an airline website which just rips the info from Timatic, and it says that transit via either SGN or HAN to PQC is acceptable without a visa, but the booking must be one ticket, flights on the same day and airline staff must escort passengers during the entire transit process (i.e. until they are airside for the domestic flight). Nothing said about the other way around (viz. departing PQC).