I don’t think you have to worry about the 5-6 CR Rabbi’s who disagree with you. The The Gur Aryeh (Maharal), The Maskil L’Dovid and Divrei Dovid (Taz) certainly did not learn Rashi like them (Obviously neither did the Ramban).
You haven’t been following the long discussion until now.
To summarize:
Rashi on Vayechi is quite ambiguous, and can probably be understood either way.
Rashi on Taanis however is simply understood to mean that Yaakov is physically alive, since he explains the Gemara that the only reason why Yaakov was embalmed and buried is because “he SEEMED dead, though really he was alive” (נדמה להם שהוא מת אבל חי הוא) [– as OPPOSED to other meforshim who hold that Yaakov was embalmed and buried because he was physically dead].
Maharsha understands Rashi this way (which is why he says that Rashi’s pshat is דוחק, and gives his own pshat). Artscroll understands Rashi this way (I’ve quoted the footnote many times). Rif to Ein Yaakov, Etz Yosef, Iyun Yaakov and Ohr Hachayim all clearly hold that יעקב לא מת is literal, and ויגוע means that Yaakov was in a deep state of sleep.
[None of the meforshim that you mentioned (גו”א, משכיל לדוד, ד”ד) quote Rashi on Taanis (נדמה להם), rather they are being mefaresh Rashi on chumash. Even if you were to find a meforash who interprets Rashi on Taanis to mean spiritual, that is definitely not the פירוש הפשוט of Rashi there, as I have shown in the previous paragraph.]
The answer to Philosopher’s question (that later it says that the sons saw כי מת אביהם) is obvious after reading the Ramban: The possuk is only writing about how Yaakov seemed to the sons’ perspective — they looked at Yaakov and say כי מת אביהם, which doesn’t necessarily reflect on the reality.
This answer of the Ramban solves the issue from this possuk for all the opinions in meforshim, including the literal interpretations. Ramban’s own opinion (which seems to be cryptic and not clearly fitting with either interpretation) is irrelevant to this point.