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.

A SINGLE AI-AT soldier doesn't attack Marid/Gorgon/Marshall on his OWN if not being attacked or discovered.

2 or more AI's in the group, and AT WILL attack them even if not discovered.

The issue is only with single unit "groups".

Tragicomic ragdolls do break the immersion. I don't mind the occcasional weird poses that much, but the fingers... oh man.
I hope it can and will be fixed somehow.

Just order them to "Relax" and they'll keep distances.
You don't have to use "Column" formation when driving on the road. They form column automatically when not in danger.

If I remember correctly from my time in the army, we were always in a "safe mode" when moving troops in a column, until we were attacked. And when attacked, no-one stayed on the road (..or the officers were very very angry...).
In Arma 3, even long convoys work perfectly if you know what you are doing.

The only and pretty major Problem is when a vehicle gets stuck against an obstacle, for example in a village or when trying to get back on road after an attack, it really gets stuck. A single rock can destroy everything.

The AI driver seems to think it's still going forwards when the front wheels are spinning. It doesn't try to back up or anything to get around the obstacle.
And the rest of the convoy is lost forever.