IIRC officers now start with one extra skill at level 1.
This was true since 0.8.0 (maybe even before) so nothing changed in Starsector. It's just that when I use save transfer, all officers lose 1 skill point. I've noticed that lv1 officers become lv2 after they are loaded but with unchanged skills (resulting in losing 1 skill point also).
Edit:
Same thing happens with just console commands, save transfer, lazylib and ship/weapon pack. For some reason, save transfer doesn't load anything except character exp and skills if ship/weapon pack is disabled. So I left ship/weapon pack enabled.
I've also noticed that IBB bounties stopped appearing in mission boards after load. I've played for some hours but it may be that I just couldn't find any yet though.