I heard in the name of the late Mirrer Rosh Yeshiva, Rav Nosson Tzvi Finkel zt"l, the following about the difference:
The expression מפרש בגמרא is used to refer to an explanation for a local concept or word that the reader wouldn't know otherwise.
The expression בגמרא מפרש is used to address a challenge that the reader might have.
I don't know what ...
The general assumption made while learning rishonim (and even more applicable to ammoraim and tannaim) is that they meant what they said, they are consistent with their own shitos/halachic positions throughout their commentaries, and that they knew all of (or most of) the alternative explanations and still chose to explain it the way they did.
So when Tosfos ...
The relevant part at the beginning of Rashi reads: "And this is why he was punished by having his mouth sawed, because he called the Jews...". So Rashi is explaining not why he died or his punishment as a whole, but why specifically his mouth was sawed.
The Sefaria translation makes the same point a little earlier:
He died specifically as this ...
The mizrachi explains rashi to be saying that:
בזאת גימטריא שלו ארבע מאות ועשר רמז לבית ראשון. דאל"כ הל"ל כי בענן
אראה על הכפרת ובפר בן בקר לחטאת שפירושו שלא יבא אל הקדש כי אם בענן
הקטרת ובפר לחטאת ובאיל לעולה בזאת למה לי
"''בזאת' is the numerical value of 410 alluding to the first temple' For if it wasn't so then it should have ...
As a general rule, unless specified otherwise, d'vash will mean fruit honey,
particularly date honey (see shiva'as haminim where d'vash is reffering to dates),
and also fig honey (a few examples are found in the gemara with stories relating
to figs' honey).