OP, just keep in mind the line right before the part about modifications: “Academic requirements that the recipient can demonstrate are essential to the instruction being pursued by such student or to any directly related licensing requirement will not be regarded as discriminatory within the meaning of this section.”
This is the part that allows an institution to impose a degree requirement without a course substitution if they deem it essential. For example, a pre-med major is not going to be approved to sub out of Anatomy & Physiology, because that course is essential material for such a major. It sounds like your son’s institution is making this argument, but they can’t do that without a reasoned review of your son’s request. And I’m highly suspicious of their assertion that public speaking is essential to ALL majors at their university. That tells me they aren’t doing an individualized assessment of your son’s accommodation request, so I would push back hard on that point. I hope you find a resolution in speaking to someone higher up at the university!