Julia, you are correct to notice that transparency is not working the way you are expecting. This problem seems to have started with SU 2017.
For demonstration I have created a (somewhat goofy) test model with transparent windows on two sides of a building.
transparency test.skp (233.2 KB)
This PNG image was created with SU2017
The alpha channel in the SU2017 PNG is a solid black region.
The PNG of the same model in SU2015 looks like this.
and the alpha channel in the SU2015 PNG looks to be correct.
I have no idea why this functionality was changed for the 2017 and later editions of SU.