Ok, so I managed to edit the starting feats without changing any utc files. I simply wasn't overwriting my Feat.2da correctly. The "granted" columns will set the level you gain the feat for each class, and "list" columns will define if it appears on that class' list. For example if I set the columns jcn_list = 1 and jcn_granted = 2 in the row for Toughness, then the Jedi consular will have the Toughness feat on their list, and receive that feat at level 2 for free.
EDIT: -1 in the "granted" column will mean the feat is never given for free