Gemara Eruvin 7a: "Rebbi Akiva picked an Esrog on the first of Shevat...."
Why does Rashi explain that "the entire tree is called Esrog" (Eruvin 7a) -- that is, Rebbi Akiva harvested an entire tree's worth of Esrogim, and not explain simply that Rebbi Akiva picked a single Esrog (as other Rishonim, such as the Ritva, explain)?
Also, in Rosh Hashanah 14a, Rashi says "Esrog" means "the fruits of an Esrog tree," which seems slightly different than his explanation here.
This is discussed (of all places) in my Sefer on Chulin, Marbeh Chaim, third Perek, #16.
I begin with the assumption that in Rosh Hashana, Rashi assumes like the Ritva that he only collected a single Esrog (or two), which is why he explains the word to refer to "fruit of the tree." Only in Eruvin does he assume that he harvested "the entire tree."
The key problem that I identify is the fact that Esrog is considered like a vegetable ("Basar Lekitah") and yet has its Rosh Hashanah in Shevat (like a fruit).
The following Chakirah emerges: is it a Halachic vegetable for Ma'aser but the physical tree forces the unnatural Rosh Hashanah of Shevat; or it is a Halachic tree that really is obligated in Ma'aser from the time of "Chanatah" but has "Lekitah" as a unique detail in its "delivery time" due to the pattern of long duration on the tree, and is only coincidentally "like a vegetable."
According to the first approach -- that "Lekitah" is intrinsic and defining of the Chiyuv Ma'aser -- then the Lekitah of the majority of the tree would be its true Zman, and would force the Mi'ut to honor the same Zman.
If "Chanatah" is the source of the obligation but delivery is measured by physical harvesting, then each Esrog would depend on its individual day of collection.
In Eruvin Rashi assumes the first approach, so he speaks of harvesting the tree at once. In Rosh Hashanah he assumes the second approach, so he can speak of collecting individual Esrogim.
In the Sefer I elaborate on the differences Rashi sees in the Sugyos, but more simply we can say that in Rosh Hashanah he is reluctant to make it a true vegetable, because the Sugya explains that the nature of trees is to absorb water from the ground and generate nutrients in a certain pattern. Since Esrog grows physically like a tree, it needs to be measured intrinsically by Chanatah, in which case "Lekitah" must be a special dispensation for its late delivery.
In Eruvin, he feels more fealty to the language of the Mishnah in Zera'im that says that Esrog is like a vegetable for Ma'aser. So he explains it as a true vegetable.