That is why the Minhag (of those who put on both) is generaly restricted to Rabbeinu Tam.
As to your earlier question, I understand it the way I understand many Derabanans. Until the Rabanan codified and solidified the Takana people did the Mishmeres Limishmarosai on their own and applied it according to their conditions. Perhaps with this too, it was never a crystalized Shita and there is an Inyan to both. Some did one way, some did the other way and others did both, or more.
This is why it was possible for Rashi and Rabbeinu Tam to argue about it. There were many varying Mesoros and both of them set out to set it straight once and for all.
The same is said of the Shvarim and Truah. There were two Mesoros and the Gemara says that we do both due to the Safek. But the Zohar Hakadosh says that there is an Inyan to both.