Is there any difference at all between stats that are naturally max'd and stats that are max'd only through items?

For example:

Con - 18(20)
Int - 18(23)

Will the above have worse stat gains overall than

Con - 20(20)
Int - 23(23)

Same goes for save vs spell, regeneration, etc.

Purely based on gains...

You have to keep those items on to be at those higher ranges. But other than the obvious, no. There is no difference.

Except in the case of a Shapeshifter. Where it goes by your form stats (while in form), and your natural stats (not your natural + magic) stats. Which is a good reason to have max stats as a Shapeshifter.

Out of form it is the same as everyone else.

Gains can go from form stats? If I'm in croc form with 25 con, my hp gain is calculated with 25 con?

So you don't have to revert to gain anymore.

Let's say you are a gnome with 22 wis and +3wis eq. If you gain in form, you get 4 practices. If you be out of form while gaining, you get 6 practices. Same goes for con. If you have lost some con and you are covering it with items, you won't get the benefit of the items while you gain in form. So better to have max stats or revert before gain.