Yeah, it doesn't mean TotJ or KotOR or TOR are officially canon, just that the post-Disney Story Group is taking pieces from those stories that they think work with the new universe they're building, and then twisting them to fit their needs. Malachor is already very different from what we got in KotOR II, for example.
If they do a show set during the last days of the Old Republic (which in the new canon seems to be different from the Republic established one thousand years before TPM) I'd actually really like to see something similar to John Jackson Miller's Knight Errant, about a young Jedi trapped in a Sith-controlled region of the galaxy in the dark age of the Old Republic, around one thousand years before TPM.
Hopefully they just ignore anything from Jedi vs. Sith. Blech.