Adding my two cents as well, so far many FAQ and Rules questions have been answered by James Jacobs, while the official FAQ are answered by someone else, they merely repeat in a more formal manner what J.J. already answered in a forum post.
He's the only one actively answering on the forums as far as I know, and I haven't seen (take this with a grain of salt, I'm far from reading every post from J.J.) him corrected by someone else from the Rules team at Paizo, so far his words are taken as
ruling by the community.
Besides, what he said is basically written in the SDR under the Ability Score rules. Unless there's an exception like the Headband of Vast Intelligence.
But OP said he doesn't wear a HoV but a house-ruled magic item giving a +2 to his Int score. This means it would retroactively give him skill points he could allocate as he wants to.
Now his question was if there's any way in PCGen to link an item to what has been retroactively given by this item (in this case, skill points are the only thing that needs tracking beside the usual modifiers from the +2 to Int). Paul Grosse answered that
for now, there's no such way to track it beside some work-around (tracking it in the description tab of the item, etc). This could become a nice suggestion, not a high priority one but eventually, it would be nice to be able to track this kind of thing.
PS: two of you may receive this for the second time, sorry about it, for some reason my e-mail wasn't registered anymore.
- PCGen User 8-)