Thank you for the response, Knight. The particular point of confusion I had was mostly cleared up in the revised Gun Rights pamphlet, specifically -

Transporting within PA: Long guns MUST be unloaded
(clear chamber and no magazine in weapon) and for magazine
fed weapons any loaded magazines must be in a separate
container in order to be transported in vehicles within PA.
Handguns may be loaded while in a vehicle only if the person
in possession holds a valid PA LTCF or a carry license from
any other state.

The confusion was over 'magazine fed weapons.' The original pamphlet was a bit confusing as to whether it referred to all magazines or only to long gun magazines. I am assuming that 'weapons' are long guns as opposed to 'firearms' (hand guns) in which case I'm good to put the mags in the case with the AR pistol. In any case thanks again for the response and for putting together the pamphlet.