–Every college has its own system for calculating GPA.
–And FWIW I’ve heard a couple of admissions officers say that they do include theology/philosophy as core classes so not every college will “throw them out” of the equation.
–All you can do is send in the transcript and let each college do as they will. It isn’t worth spending a lot of time on things that are out of your control.
–Congrats on MSU. (isn’t the OP’s son you referred to in post #25 your son?)