This explanation (which the Chasam Sofer says should be followed l’halacha) seems to fit exactly the question posed above. The Jew who stopped in Marseilles for Shavuos should therefore keep both the stringencies of Eretz Yisrael and those of Marseilles. It would seem that he should refrain from performing melacha even in private on the second day of Shavuos, like the Jews in France, and also put on tefillin, like the Jews in Eretz Yisrael.
However, Rabbi Stern concludes that many Acharonim dispute the Chasam Sofer’s ruling. Therefore, the Jew in our story should follow only the customs of Marseilles, as if he had already reached his destination.