Sorry about that Will! I got too focused and wasn't reading as clearly as I could have.
I think I understand now. You are seeing additional polygon features selected around the the spatially filtered polygon boundary. I believe this is caused by the polygons having overlapping features. By default, the spatial selection does an INTERSECT, so even if the boundaries are overlapping by just a few pixels, it will be captured.
We have open enhancements to include additional operators such as 'completely contains' which I think would solve this issue.
A workaround would be to set up a foreign/primary key between these two polygon layers and use field filtering instead of spatial filtering.
Are we on the same page now?