Far from made up, Affliction was a major org that had half of the top 10 HWs in the world at the time. Shooto was a fine org, but I don’t even know if I’d say it was the premier org for lighter weight classes at the time (although it certainly was a very solid org with a good roster). Way back in 2001, a lot of the MMA rankings piled anything below 205 in one ranking. Militech was ranked right at or near the top, and he never had a single fight in Shooto.
But this is all expected behavior from you. GOAT criteria is subjective, but should at least be consistent. If you’re going to be counting Shooto belts in any way, shape, or form, then you should be applying that criteria to every GOAT candidate you assess. But you don’t do that of course, because you don’t like the result.
What about Fedor’s RINGS titles? Surely you must count those then?