This question is dealt with at great length in the Sefer "The 13 Principles of Faith" (Gutnick edition) by Rabbi Chaim Miller in the Eighth Principle, Lesson Seven, based on the teaching of the Lubavitcher Rebbe.
He summarizes the chapter as follows:
- The Sanhedrin of each generation was authorized to overrule any of the derived laws of the previous generation.
- Therefore, when derived laws were lost, it did not represent a crisis because the current Sanhedrin was not bound to the in any case.
- Furthermore, when laws were forgotten it was often the case, not that a single legal opinion was lost leaving us with no data, but merely that the consensus of opinion was forgotten.
- While the Sages of each generation had the right to disagree with their predecessors about derived laws, it was nevertheless preferable for them to agree.
- Nowadays, Rabbis do not have the right to disagree with the ruling of the Mishna, Talmud and Shulchan Aruch since they have been universally accepted by the Jewish people as binding.
The sources he bases himself on in the Rebbe's teachings are: Sichas Yud Aleph Nissan 5737, par 19-22; Sichas Acharon Shel Pesach 5737, par. 43-50; Sichas Shabbos Parshas Matos 5742, par. 25; ibid 42-46; Sicha of 15th of Tammuz 5746-Al Davar ha-Mahaduros de-Sefer ha-Yad le-ha-Rambam
To specifically answer your questions regarding which Tefillin Moshe Rabeynu wore (the Rebbe asks this question in the first Sicha above): even if Moshe wore Tefillin of Rashi, Rabeynu Tam would still be allowed to argue.
Two stories to illustrate this point:
1) Seder Hadoros (year 4930) brings the story of an argument between Rabeynu Tam and other Rishonim regarding how one should tie the knot of the Tefillin. Eventually Moshe Rabeynu himself is called down from heaven and asked his opinion. He testifies that he personally saw the back of Hashem's Tefillin shel Rosh, but Rabeynu Tam is not persauded. In the words of the Seder Hadoros: "Rabeynu Tam got up like a lion and said Moshe Rabeynu you are mistaken!".
2) The Chossid R' Hillel of Paritch was a devoted follower of the Tzemach Tzedek. The was once a dispute amongst the Chassidim how to interpret a certain point of one of the Rebbe's discourses. When they asked the Rebbe himself what he meant his response favoured the other Chassidim's aproach and not R' Hillel's. However R' Hillel refused to retract from his position, explaining: "When the Rebbe says a Chassidic discourse the Torah is being given from Sinai. But like all words of Torah, it is crucial that we understand them, and that means using our own brains. So the Rebbe has his understanding of the discourse - said this morning at Sinai - and I have mine."