Indeed consuming protein molecules which contain glutamate is different from consuming free glutamate in the form of MSG.
We can draw a ready analogy to saccharides. It is like denying the effects of sugar because indigestible complex carbohydrates are made of sugar and do not produce those effects. "A blood sugar spike doesn't exist because cellulose is made of sugars, and I've eaten a large bowl of moistened sawdust without experiencing such a spike. It's probably an imagined effect or maybe caused by something else, such as a response to anti-caking agents in the sugar."
Why is MSG used in the first place on foods which already contain glutamate? For instance, why is it used in Vietnamese lemon grass chicken recipes, given that chicken protein has tons of glutamate? It's because the glutamate that is locked up in protein doesn't produce the taste effect of MSG.
So why don't these naysayers deny the existence of the taste effect of MSG also?
As in: "Gee, I don't believe that MSG can possibly be a flavor enhancer, because boiled chicken breast contains copious glutamate and yet tastes bland. People who say that flavor is enhanced by MSG are just imagining it due to confirmation bias fueled by mass hysteria."