The gemara discusses the amount of "teruma" that needs to be taken from the Todah breads and contemplates learning out the amount from terumas ma'aser. The gemara suggests learning out from challah which is also called teruma, to which rashi explains that the shiur would be 1/48th. Both Rabbeinu Gershom and the kesav yad of rashi explain that it would be 1/24th [This is not a consequential difference since the shiur for challa is 1/24th for a ba'al habyis and 1/48th for a nach'tom. The Nodeh B'Yehuda suggests that according to the Rambam in pirush hamishna the real shiur for challah is 1/48th, just that the women baking will tend to be cheap and if we tell her 1/24 she will at least give 1/48th - that is why rashi picks the number 1/48]. The Nodeh B'yehuda (tinyana y.d. 201) asks that challah doesn't have a shiur according to the Torah, similar to Teruma gedolah which has no shiur. Since the shiur of 1/48 is only Rabbinic, how can the gemara suggest to learn out that the shiur of the Todah breads will also be 1/48?
The Nodeh B'Yehuda suggests something that "no commentary or posek had already said". The mitzvah of challah contains two parts. One is to remove the status of tevel on the dough thereby permitting it to be eaten. The second is the aspect of gifting it to the kohein. The first aspect has no shiur, similar to Terumah where even the smallest amount renders the remainder chulin. But, the shiur of 1/24 or 1/48 is a Torah obligation as the minimum amount to be given to the kohein. However, the shiur of 1/24 is the minimal amount of the minimum amount that is chayev in challa (isaron), that is necessary to be considered a "giving" to the kohein. On a Torah level it wouldn't matter whether one is kneading 1 Isaron or 50 Isaron, the amount that must be given to the kohein is the same - 1/24 of an Isaron. The Rabbonon then came along and required that one give 1/24 of whatever amount they are baking to the kohein. The son of the Nodeh B'yehuda elaborates about his fathers opinion and writes that although there are two parts, they must go together. One cannot separate a tiny amount to be matir the dough to eat and then separate 1/24 to give to the kohein. One must separate initially 1/24th in order to fulfill the mitzvah properly, but if they had already separated a tiny amount, there is no way to add on to that amount and properly fulfill the mitzvah. According to this approach, if one would separate a tiny amount to be given to the kohen, it is a מעוות שלא יוכל לתקון and at the time of separating they are inevitably in violation of the mitzvah to give a proper amount of challah to the kohein.
The Mitzpeh Eisan says that this peshat has already been said by the Tosafos Rid in Kiddushin 58.