At first glance this chiddush seems to be a machlokes Tana'im later in the masechta. R' Meir allows a sukkah to be made on top of an animal; R' Yehudah does not. The gemara (23a) explains that we learn from the pasuk, "Ba'sukkos teishvu shivas yamim," that a sukkah must be usable for the entire seven day duration of the chag. R' Yehudah holds that since one is not allowed to climb on an animal on Shabbos and Yom Tov, a sukkah built on top of an animal is not usable for seven days. R' Meir counters that the prohibition of climbing on an animal is only a din derabbanan; you can't say a sukkah does not meet the d'oraysa criteria of being usable for seven days just because of a derabbanan disqualification. Apparently, R' Yehudah holds othewise -- the din derabbanan that prevents one from using a sukkah built on an animal does in fact negate the d'oraysa kiyum of sukkah, exactly like the chiddush of the Pri Megadim.
Yet maybe things are not so simple and one can be mechaleik. The requirement of having a table within the sukkah is a din in hilchos sukkah. Perhaps in principle even R' Meir agrees that failing to meet a derabbanan criteria of hilchos sukkah can negate the kiyum d'oraysa of sukkah. However, the prohibition of climbing on an animal is a general din in hilchos Yom Tov. R' Meir perhaps holds that a din derabbanan of hilchos Yom Tov cannot negate a kiyum d'oraysa of sukkah.
R' Akiva Eiger writes that even though Chazal disallowed blowing shofar on Shabbos lest one come to carry the shofar, if one went ahead and blew, one fulfills the mitzvah d'oraysa of shofar, albeit at the expense of an issur derabbanan. Against the Pri Megadim? Again, maybe not. The issur of carrying is a general din in hilchos Yom Tov, not a din in hilchos shofar. A violation of a din in hilchos Yom Tov does not have the power to negate a kiyum d'oraysa of shofar or sukkah.