A lot of folks are latching on to the "hiding place" theory, and that could very well might have been one of the use cases. But as the article points out, the lack of a second exit makes that unlikely.

I would like to offer a competing theory. These are thermally stable storage places for perishables.

As heat transfer is directly proportional to surface area, the ideal vessel that maximizes the volume / surface area ratio would be a sphere (like some cryogenic tanks for rockets). But if you don't have the technology to make that or a cylinder, then the best you can do is observe that lowering surface area helps and make smaller, long rounded passages to try and optimize a ratio that you don't understand by feel.

I think it's more likely that these are are ancient fridges / hot boxes than a way to spiritually experience rebirth. I think a thousand places to store hay for horses and cheese for your family is far more likely.

Could these be boltholes? Yes, but how frequently were places getting invaded? War was mostly siege based and was fairly infrequent for a given city / place (i.e. even if the polity next door was under siege at the time. You weren't) Winter and summer - on the other hand - were and are yearly guarantees.