Now we can explain Rashi: Rashi definitely agrees that when it says "אך" it is limiting Shabbos and not the Mishkan as the Ramban asserted and like we see in the Gemara that it is permitting פיקוח נפש on Shabbos. However when the Tosefta says in the name of R' Yosi that from this pasuk we learn that עבודה and מילה override Shabbos it doesn't mean that in this pasuk it says that עבודה and מילה override Shabbos - because we have other psukim for that as we learn elsewhere in the Gemara [as noted by the Chasdei Dovid]. Rather it is telling us that the basis from which we are enabled to derive from other psukim that מילה and עבודה override Shabbos is the word "אך". Because as we explained if not for the fact that it says "אך" we would view Shabbos as being a mitzva that is "outta this world" [i.e. from Olam Haba] and then עבודה and מילה would not be able to override it. The same goes regarding פיקוח נפש. If not for "אך" we would say that it is a mitzva from Olam Haba, an anomaly, and thus there is no exemption even for פיקוח נפש. Only because of "אך" we can limit Shabos and categorize it together with other mitzvos and thus פיקוח נפש takes precedence as do עבודה and מילה.
On the other hand from that very limitation of "אך" it emerges that one may not build the Beis Hamikdash on Shabbos. If not for "אך" one would say that since this melacha beings the שכינה it is permitted on Shabbos because it is not a contradiction for the Olam Haba'esqe Shabbos. But since it remains in the class of regular mitzvos and the rule is that an עשה does not override a לא תעשה that has כרת, the building of the Beis Hamikdash does not override Shabbos.
So Rashi was right that based on the pasuk of "אך" we have a basis to forbid the building of the Beis Hamikdash on Shabbos even though Rashi agrees that the limitation and exclusion relate to Shabbos, as we see from the Gemaras that derive from "אך" that פיקוח נפש, עבודה and מילה override Shabbos.
So Rashi's understading of "אך" is correct and he is also is saved from the questions of the Ramban from the various sugyos!!
But still there would be room to say that the מיעוט of "אך" that was said regarding Shabbos means that we shouldn't be stringent because of the Olam Haba aspect of Shabbos. Through this there is room to override Shabbos with פיקוח נפש, עבודה and מילה. However when it comes to the building of the Beis Hamikdsh on Shabbos, where as far as Shabbos is concerned there is no reason to be stringent [because the Beis Hamikdsh brings the שכינה so the building is not a contradiction to Shabbos] - who says that we can learn from "אך" to be stringent and forbid the building? THAT is why we need the psukim at the beginning of parshas Vaykehel to teach us that the building of the Beis Hamikdash doesn't override Shabbos. But after these psukim it emerges that the word "אך" limits because it is telling us not to view Shabbos in the context of Olam Haba but just in its Olam Hazeh definition and thus to forbid its building on Shabbos. So Rashi was correct in telling us that the word "אך" teaches us this halacha because "אך" is not telling us a practical law but a definition [that Shabbos has an Olam Hazeh and Olam Haba aspect and "אך" limits its application to its Olam Hazeh defintion].
We can also answer the questions of the Aruch La-ner:
The two sources that teach that the building of the Beis Hamikdash doesn't override Shabbos aren't talking about "דיני דחייה" per se, which is the subject of the sugya in Yevamos, but rather whether as far as the ESSENCE of Shabbos we can allow בנין בית המקדש. Even after we prove that as far as the essence of Shabbos goes, one may not build the Beis Hamikdash [because of "אך"] maybe there is still a halacha that the בנין is דוחה שבת. THAT is the topic of the sugya in Yevamos which teaches that it may not [because אין עשה דוחה לא תעשה שיש בו כרת] and the only question is regarding מחמר which is only a לא תעשה without כרת.
We can also answer the questions of the Aruch La-ner:
The two sources that teach that the building of the Beis Hamikdash doesn't override Shabbos aren't talking about "דיני דחייה" per se, which is the subject of the sugya in Yevamos, but rather whether as far as the ESSENCE of Shabbos we can allow בנין בית המקדש. Even after we prove that as far as the essence of Shabbos goes, one may not build the Beis Hamikdash [because of "אך"] maybe there is still a halacha that the בנין is דוחה שבת. THAT is the topic of the sugya in Yevamos which teaches that it may not [because אין עשה דוחה לא תעשה שיש בו כרת] and the only question is regarding מחמר which is only a לא תעשה without כרת.
WOW!!
[עפ"י תורת מו"ר הגאון הגדול ר' ד"י מן זצ"ל]