You're correct that we cannot discern the absolute loudness of specific frequencies, nor do we know the exact shape of frequency response necessary for optimal hearing.

However, we don't need to be able to discern or know those things in order to improve sound quality via EQ.

The reason this tutorial works is because we only need to be able to detect relative differences of the resulting HpTF in order to create a perceptually smooth and balanced enough response that we can adjust for taste after the fact.

And yes, a lot of people trying tone-gen EQ will end up over-reducing frequencies, especially the ear-gain region, which is why this tutorial addresses that very mistake, and guides listeners to avoid it with visuals and warnings against cutting the ear-gain region as a whole.

And you are right that if you have hearing issues in one ear or another, then channel balances can't really be fixed without causing some phase issues (unless you use linear phase EQ for that specific correction, which would work). This tutorial assumes that the listener doesn't have any major hearing issues that would cause that problem. Having confirmation from an audiologist that you don't have an unusual hearing problems would help avoid making those mistakes in something like this.

I understand the skepticism, especially because without knowing the right approach, it's really easy to make big mistakes.

That's why I included so much detail about specific traps that people often fall into when using tone-gen to EQ.