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what does this mean? "BS or MS in this degree or equivalent with high GPA, or graduated from top school"

Are they saying the guy needs to be from a top school or have a good gpa? Does that comma make a difference?
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nerdikarpAre they saying the guy needs to be from a top school or have a good gpa?
Yes. Apparently you are qualified if you've graduated from a top school even if you have a low GPA. The writer may not have intended it to say that, but that's what it says. With or without the comma, it makes no difference to me.

CJ
Comments  
Yes. CJ is right, even if I were unsure about the context, I am sure that universities ranking is a factor of admission even you haven't very good GPA.