From what I've seen, it appears Strange's structures will clear out pre-existing water from inside them. For example, a ruins on the edge of a river, or underground lakes for the foundations.
However, it also seems that waterlogging is an exception to this rule.
While regular water blocks are removed, any blocks which have become waterlogged during generation remain that way, and thus pour water everywhere.
Some examples:
In a foundation.

In a surface ruin.

This is a vanilla bug that can sometimes be seen in villages, too. Nothing we can do about it, sadly.

Dang. Good to know, at least.