Again, retroactively, his further intentions pertaining to new information not previously given to us as an audience is all assumption.Well I mean it's not really assuming, he explains his intentions in the finale about hiding the truth of the Multiversal War from the TVA and keeping the rise of Kang from happening. It's why he founded the TVA and made the Sacred Timeline. We also know the TVA cant track time travel unless it branches otherwise Sylvie would've been found beforehand. I am however assuming he knows it's possible and that he hid the fact that time travel can happen without branches and kept it on need to know since only he knows.
That being said obviously we should wait for Quantumania, Loki S02 and whatever else will deal with this stuff before we say for sure. It's just a theory as to why Kamala can time travel without creating branches and why the TVA would've been unaware of that possibility under HWR.
It's a gap that hasn't been filled yet between this and how Kang plans to do it his own way.
I fully expect this to be explained.