it very well could have been, but I have seen a huge inconsistancy with nut height in the last 12 years I have been looking at Fender guitars.
My first (real) Fender guitar I bought was a Deluxe Powerhouse Strat ('98), and I have had many (guitar tech) people/friends ask me who set up my nut. FENDER DID!!! It's factory, and it looks better than any other factory Fender I have come across in the last 10 yrs!!! I don't know if it was a fluke, or an example shown to the factory workers, but my guitar's nut was shaved and set to a level that I still havn't seen repeated except on $2000+ range Custom Shop Strats (which has blown me away FYI). My Jag-Stang didn't have this level of detail to it's nut, nor did my buddy's American Deluxe Strat (which pissed him off... but,... he did buy his online...) All I'm saying is that you never know what yr getting unless you buy it firsthand and can inspect the damn thing. I lucked out on the nut on my Strat (BIG TIME!!), but my JS had a rather lousy type nut height that I had to shave down and adjust the truss rodd, etc....(which sucked... (BIGTIME!!!!)).
Overall, I can't say #### for what the Jag-Stang's inital height was or is. I can say that only 2 to 3 (or more) companies in Japan have manufactured this guitar (for the masses) and we ultimately don't know what the height was supposed to be... unless we can measure the originals!! Those are now currently in the hands of REM and the Fender museum. We would need those to make a "proper" measurement. Otherwise, find an old '65 Jag and make measurements, and hope for the best....