If you want to have an easy way out of this, just set a rule for yourself that assault transports never leave stand-down mode, no matter the situation. Gun is removed, problem solved!
I just never use Assault Transports. This is like a player-enforced Nethack's conduct.
Oh yeah it's also the best way to scout. Load it with scouts and you can get a 4 or 5 jump headstart before it pops.
Though the rest is true, this I'll disagree with. Mk IV Scout Starships are the best way to scout since one of them can do every planet in a 120 planet galaxy by the ten minute mark.
Hm. I never unlocked even MkII scout starships (neither cloakers). 5,750 K for fully scouted map? I dunno; if I just want to have the whole galaxy scouted, I would play with partial fog of war, right? Or maybe the partial fog of war shows also the ships in every planets? But isn't it the "no fog of war" setting? I never use them, so I can't tell. Anyway, is this worth? Near 6,000 K for full scout? Who use them? Is that really interesting? Tell me, please.