I think that if a hat can be a portal to a room of doors which leads to other worlds then all these wells probably have that same sort of connotation.
To me, the wells are a different form of travel between the worlds.
It makes sense to a degree, based on how quickly Thomas disappeared in ‘Price of Gold’.
However, part of me thinks these wells just might be interconnected among the realms of FTL. Kind of a`la the pipeworks in Super Mario. You go in at point A & show up at Point B or something along those lines. It would be a rather useful mode of transport, nice & stealthy.