As for the qoute that was 00646 provided from MN.
I admit that I am not entirey familiar with MN as opposed to the Rambam’s other writing since I was told by my Rabbeim that the Mesorah was not learn it without a Rebbi.
However I would offer that I do not think that it’s a contradiction since the Ramchall in Mamar Al Aggadita states that at times the main purpose of Chazal were to write “Sodos” so they woud not be forgotten.
However since they could not write this openly they used the “language” of their time to write things so that it would not harm those who did not understand the true meaning while it would be there for those on a sufficient level to understand the real intention.
Based on this it would seem to me that the Rambam you are qouting in MN is merely stating that when Chazal wrote things at times they only wrote according to what was the science of their day, since their intention was not to write things from MEsorah.
However in reality Chazal knew far more then what was scientifically known in their day, which is basicaly the position of the Rambam in Chelek and what is explained in detail by the Ramchal.