the issues are most likely due to the way blender exports stl files.
Maybe need an update version or a 3rd party add in to do a better job ?
That said the building look pretty good to me :-)

I've only ever designed in openscad, which only produces perfect solid models. So that's not something I have ever had an issue with.

The easiest way to check in s3d is to do a print preview. Often the model view and print preview look quite different. the print preview is the important one :-)