Not being a lawyer and being myself a citizen from a Schengen and EU member state, I don't have any direct experience with this kind of issues so that everything I will say should be taken with a grain of salt. Still, I am wondering if it makes any difference in practice (and, incidentally, how frequently this could really happen). It seems that a long stay visa from one of the member states of the Schengen agreement (which is not a Schengen visa as the Schengen agreement only covers short stays and each member state remains mostly free to establish rules governing long stay visas as they see fit) gives you the same rights, in other member states, as a “uniform visa” (i.e. multiple entries in the Schengen area for a maximum of 90 days stay in any half-year).
This webpage from the French Interior ministry seems to support this interpretation.
According to this webpage, what you have to do to be able to enter France again after 5 months is to go back to the country that delivered the long stay visa (i.e. Germany in your example), just as an “uniform visa” would require you to go back to a non-Schengen country to avoid using up your 90 days quota. One thing I don't know is how you can go about documenting the fact that you did leave France if you travel by road instead of taking a connecting flight since there are no border controls between France and Germany. That's the main practical difference with the uniform visa situation as external Schengen borders are guarded and you would get an exit stamp on your passport but the 90 days rule applies in both cases. (You mentioned France as an example and I looked it up in French but I believe those rules were defined in some EU directives so they should apply for other Schengen countries as well.)
Most importantly, a long stay visa from Germany (or any other Schengen country) does not entitle you to stay in France (or any other Schengen country) for as long as you wish (i.e. Germany cannot deliver long stay visas for France or vice versa) so that in both cases you are really using your right to make a short stay in France. Only after 5 years of residence in Germany, will you in fact be entitled to a long stay visa in France (actually a “titre de séjour”, this is not a visa but a separate document) but this has nothing to do with Schengen, this is a EU rule that does not apply to non-EU Schengen countries (and also not to the UK, Ireland and Denmark, despite their being EU members because they opted out, see here). It probably also applies to Switzerland via their bilateral agreements with the EU but I am not quite sure. I suspect that having this right recognized might not always be trivial in practice.
Additionally, I understand that there are complex rules regarding airside transit. Depending on your nationality, you might be entitled to visa-free transit in international airports of some or all Schengen area countries, so technically needing a visa to stay in the Schengen area does not automatically imply requiring a visa in your scenario.