I just had an epiphany!

As humans have been walking on the land for a long time, these conditions is what our bodies have adapted to and rely on. Reduced bone density and muscle loss are some very common side effects with anyone spending a long time in space. It is interesting to hear about the electromagnetic effects as well, would expect a mountain of research on it over the years.

As for humans not using their internal magnetic guidance, we have roads and street names to get around instead. These types of functions only grow when they are used, like a muscle. I expect there would be some dormant capacity for some that wanted to train in it, but until the effort is made the body has higher priorities to put its resources into, a bit like our shrinking appendix in the digestive system.