In Europe there is no strict separation of "domestic" vs international (in reality: Schengen vs. non-Schengen) all the way to luggage collection. By the time you reach the baggage carousels, you have already cleared immigration (where required), and there is no longer any segregation between passenger types/origins once you can collect your luggage.

Luggage checked in within the EU customs area has a green edge.



Passengers exiting the secure/airside area of any EU airport with luggage having labels lacking this green edge - or with the luggage label already removed - will be very conspicuous to customs personnel.



And it's not like in the US where every passenger has to make a customs declaration, and/or interact with a customs employee, even if this is just to hand over a card stating they have nothing to declare (even though I think this is no longer the case in the US?). Customs will intervene where they have reason to, rather than making a big show to eyeball every single arriving passenger. But, if they are going to make a random intercept, they can instantly tell from your luggage label (for example) whether your luggage was checked in outside the EU customs area.

So, logistically there is no issue with funneling "domestic" passengers through the same path that passengers arriving from outside the EU must follow upon arrival at Marseille, to follow your example. It doesn't mean that "domestic" passengers are in any way hindered, nor does it lead to any greater workload for customs personnel.