If you don’t have the cones for a specific frequency of light, how are the corresponding neurons going to light up in an fMRI?

Yeah, I understand the limitation. But that is an irrelevant objection (is my point), since we already know that the color blind don't see the same colors - and know it at an objective level even (they can't discern them from totally different colors when asked for example).

The study is meant for people with typical vision. Might as well object that they didn't include the blind...

Blind from birth, sure. A bit off topic, but a person who has experienced colors normally and later become blind could still imagine seeing the colors, and that would likely produce the same activation pattern, at least in some parts of the brain.

Then there’s the fact that some people are unable to distinguish between blue and green colors, because their language uses the same word for both. They simply cannot perceive the colors being different. How would they compare?

Is my blue your blue? Yes but only if we see the same blue.

That's what the study addresses (even if inconclusively).

The question is how "but they didn't include color blind people" has any relevance to the subject.

For color blind people we already know that they don't see the same colors, so the answer for them is trivial. They can't even decode the same input, so nobody expects them to have the same color qualia as someone who does.

The purpose of the study is to examine the color of people with same typical vision capabilities. So regarding the objection, it's like some team doing a pitch perception study and someone asks why the deaf weren't included!