Perhaps a 2da that was overriding the factions tables, especially 'Neutral'. The girl and the cats are spawned as 'Neutral' (all 50). The mod never alters a whole faction.
As for classes choices read the presentation if you wish more information about balancing your party.Besides all companions can be multi classed so you can tweak them later on. So play the class you wish.
Don't worry too much about alignment, Don't forget that your official alignment is never altered (you earn points instead). So you can adapt your behavior regardless of your official alignment. If you are LN and get madly in love with a CE girl, be nice to her
and sometimes be a bit chaotic
or evil
. It just makes things a bit more spicy
.