Disclaimer: Not sure which section this belongs in so no hard feelings if it needs to be moved.

Anyway, when visiting Solstheim in the Dragonborn DLC, we visit the Temple of Miraak. However, I don't believe this place existed when Solstheim was depicted in the Bloodmoon DLC. I never played it though so I don't know for sure. Did it exist? What was in its place? And is there any information in the lore to explain how this large temple (the underground portion, not the portion being built) suddenly appeared on the island?

-No

-The Tree standing stone

-We just never saw it in Bloodmoon because we never went underground.

The Temple of Miraak wasn't depicted in Bloodmoon. I suppose the ice covering it melted over the years, which caused the temple to surface, or some archeologists ran some excavations which led to the unearthing of the place.

Surface part was probably recently built by his "devotees", the interior however was buried (most likely by Vahlok/Dragon Cultists) beneth the Tree Stone, and wasn't recovered until Miraak need to.