There does seem to be this notion that being "too hygienic" is a negative thing because it doesn't train your immune system.
That's only kind of true. Exposing a healthy person to small amounts of weakened virus tends to build immunity. Exposing the healthy person to large amounts of the virus overwhelms the immune system and may not even lead to a strong viral immunity.
If I had to guess, eating rotten meat is something that indigenous peoples have adapted to over time (and some individuals died along the way to that adaptation) and they are resistant to the specific things in rotten meat that make modern day humans sick. I think it would be wrong to suggest the rotten meat eaters are somehow better off for doing this, or that they have stronger immune systems in general.
Immune systems aren't like a muscle that you can repeatedly train to get stronger and stronger and stronger ad infinitum.
Immunity also comes at a cost. This isn't talked about often. But it's not "Free" for your body to learn and maintain immunity to specific infections.
Especially in the last years, the hygiene hypothesis is not about a lack of immune training against harmful microbes, but a lack of encounter of so called old friends, harmless microbes.
I'm picturing a guy hauling a roadkill deer in, tossing it on a table and yelling "meat's up!" I mean, sure, they didn't have cars back then, but it's better than letting trash-eating deer meat go to waste.
I see how easy it would be for me at least to assume they had better immune systems from eating the spoiled meat. If true our modern immune systems are most likely way less effective than theirs at that time.