Not by a strict reading of the rules, no. Most DMs don't get the nuance, however, and allow for sloppy bookkeeping. Anyway, the wording is precise. A "rank" is the amount of points you put in due to leveling up your skill points. It isn't any extra points that come from feats, skill synergies, etc.
Many thanks. One more question. Is there a feat that allows a player to use their reflex save instead of their fortitude save. Trying to make a decent rogue.
No way to substitute Fort for Reflex saves that I know of, but there are ways to bolster the Fortitude save ... Unbelievable Luck will boost your lowest save by 2, and you get two luck rerolls, which may be good for spending on saves anyway.
Sorry that I can't be more precise, but I can sorta answer your last question.
There is an item that prevents you from being transformed, but I do not recall what source it was from. My brain is telling me it was something from second edition, but like I said I don't recall exactly.
It was called an Amulet of Inviolable Form. And it made you immune to having your form changed via transmutation spells and abilities. So, you could not be polymorphed against your will, but you could still be disintegrated.
IIRC, anything that gives you the shapechanger subtype makes you immune to shapechange (or at the very least you can transform back to your original form without problem)
There are PrC's that change your type this way. Don't know about a magic item though.