China sees a distinction between Civilian Vessels & Military Vessels within EEZ as it relates to FON and is raising it based on security related interests. The United States obviously (currently) does not share the same view based on it's own interests and is enforcing it's position. This is a serious, real-world, point of contention and discussion between the parties.
You cannot dismiss the dynamic of Civilian versus Military FON transit within EEZ, for the simple reason that it is a part of the current geopolitical discussion at play. It's also pretty clear why China would want to draw a distinction between the two types of shipping and why painting China as a threat to the principles of FON, full-stop, is just silly propaganda for the uninformed.
Now you can take whichever position you like regarding the above and debate current maritime law ad nauseam... But real fact is that the only law subject to eternal constant is the law of nature. The laws of men come and go and are changed with regularity. I suspect China's views on this will find their way into global policy, in some part, over the coming years.