When adding a headband of intellect the option for bonus skill points under Feats & Abilities/Misc appears.
When the magic item was created using the custom magic item tool bonus languages are able to be selected, but no bonus skill points.
OP is expecting the ABILITYPOOL bonus from select magic items to work in the customizer for generic stat boosts.
I figured there would be a entry under the misc area like DM awards where players could select where the extra points go
That’s the abilitypool feature I already mentioned. The issue is you are granting a generic bonus to an ability score, but when you select Intelligence, you’re asking for more than the Modification to the stat. That’s where the construct falls apart. I either need to create an intelligence boost only to make that work, and then make it not user intuitive or grant every stat bonus those skill boosts, because there is no easy method to limit it to just Intelligence.
There is no way to add an item under Feats & Abilities / Misc called Intelligence item skill selection and have it work in the same way that bonus skill points from favored class?