Tise mod removes most default Jedi feats (set to -1 in the jcn_granted, jsn_granted and jgd_granted columns of feat.2da) and gives bonus picks to buy them back. Those picks are set in rfeatgain.2da (jcn_reg = 10, jsn_reg = 10, jgd_reg = 11).
The game reads that for character creation and when you train a companion as a Jedi. The file can't limit it to the player, so Atton, Mira and the Handmaiden also get 10 or 11 free picks. Fixing it would need a script change, not just 2DA edits.
If this bothers you just install the mod, create your character, then uninstall it before training any companions.
https://i.imgur.com/ca85bZf.png