I always fit Tempest with Bulkheads because I don't want to "waste" an officer on a ship that doesn't constantly see action, when I'd much rather have them in destroyers or cruisers which do.
My Temps don't usually get deployed except as an escort or in pursuit.
Same ship, different role.
I suppose I can see the logic of putting autocannons on a Sunder, but I've never seen the situation you described as I never have a Sunder fighting off on it's own. And wherever possible it will have a cautious officer and be escorted by one of the above Tempests.
And in any case:
If they rush just drop shields and melt with Sunders active. Guarenteed shield overload in a few seconds.
This is also why you want to put Sabot on the wings. An instant "I win" safety net.
I don't generally use capital transports either, as I don't want to deal with the speed/utility restrictions.
A small herd of Colossi will easily take care of your surveying needs and give a decent amount carrying capacity.
Fuel is trickier, and usually the only time I make an exception to the above generalisation. But then it doesn't come up all that often as I tend not to use capitals much at all, apart from my Odyssey.
I try to use burst lasers as energy PD wherever possible, so never need to make use of the AI mod. In fact, I can't recall the last time I did use it....
Pilum however, I love. They're like the tac laser of missiles. The more you have, the better each of them becomes.
Speaking of which....