I was intending to put the test equipment in the hole.

Since "flying over test antennae" was an option, it shouldn't be a problem that there's solid ground (the bottom of the hole) underneath the test equipment.

I think the real answer is that they need more angles than keeping the aircraft flat and level and putting the antennae below it would provide. The aircraft have to be suspended anyway, so they can be rotated and have different profiles measured.