i titled it an issue with the y axis but i don't know if that's actually what it is just figured that was probably the cause but basically the underground areas are acting as though they are above ground making it snow/rain underground as well as making it so that if you sleep your spawn-point changes to the spot you slept but on the surface (if you have structures or trees above you then you spawn on top of them so its always open air above you)

i can give additional info as well as pictures if needed but its difficult to take screenshots on my PC due to some issues with image file types so id prefer not to if i don't have to and what i gave was all the detail i could think of off the top of my head so that is why i did not give those in the initial report