Yeah packages.2da has known (at least to me through previous work) problems when running out of a hak file. I believe the issue is running outside a certain index. I found that editing default packages worked just fine from 2da, but custom ones (added to later rows) weren't having their magic-related entries read properly. You might be able to work something out if you shuffle around and edit pre-existing packages but when you want to add ones lower down you might not get good results.
I tried replacing one of the existing packages with one of my new ones, and renaming my override folder so I was only using the 2DA from a HAK. Unfortunately It didn't work for me - although admittedly I replaced one of the non-functional packages left over from NWN. I'd rather not replace a functional NWN2 package, since it might be one that a player chooses for their PC.
This is a problem, since one of the companions in my current module has a custom PrC (Warsling Sniper), so he needs a new package in order for the player to level him up manually. Since I'd rather not have to instruct players to put one (and only one) of my modified 2DAs into the override folder, that leaves me with two options; strip him of his custom PrC, or create an automatic level up script for him. The latter prevents the player from having any say in how the companion levels up, but at least he retains his cool halfing-specific PrC.
I'll also have to rethink the cleric companion. He currently has the Animal and Sun domains, and relies on a custom package to auto-level him at the start of the game to get around the Air/Animal bug. However any package with Animal in it should do, since his animal companion is an integral part of his backstory.
It will be easy enough to change the fighter/weapon master companion to specialise in longswords. He currently specialises in battleaxes (the favoured weapon of Tempus), but statistically speaking a battleaxe isn't much different to a longsword, and the many fighter and weapon master packages that already exist seem to have longsword fetishes.