I can't repro That. My guys engaged EVERY time. You should do a repro mission of that situation too.
I tried AFV's, Marids, differend locations, 1-12 AI's and every time they destroyed it.
And yes, I noticed that the alone AI-AT does engage too. He just waits a bit longer, when the target is APC.
So, being "alone" is not an issue, not using launcher at APC's is not an issue.
But the rooftop placement May be an issue:
In some cases, if the AI goes prone, he loses the line of sight to the vehicle. When alone, he is not ordered to engage target that, when grouped, someone in the group would see.
If you move the AT guy on top of the "Barracks (New)" building near the one in the repro and near the edge, give him 8 meters elevation, facing south, move the AFV south facing away from the AI, so the situation is like in the repro - but now he sees the AFV when prone: wait few seconds and the AFV goes boom.