You mention shorter-ranged weapons, but the Afflictors I build don't even have PD. They have a single firing group, all-660 range or higher, depending on officer. They still uncloak point blank at times. Maybe the fact that I play more phase ships plays into this, but to me these guys are as suicidal as they've always been. This is especially frustrating when you put a steady officer on there to try and curb it - only for them not to really give chase to fleeing ships efficiently anymore, yet still die to the occasional right-at-the-end-of-combat point blank decloak blunder.
Hmm, I'm just not seeing the same thing. I've been playing a bunch with phase ships - frigates in particular - and they've been remarkably survivable, even with some of the phase cloak changes that would in theory impact that negatively.
It's *certainly* better than it used to be in 0.9.1a, though; I spent a decent bit of time making the AI respect ship explosion radius more, especially in the case of frigates swarming a single enemy, which would be particularly relevant here.
But, they will mess up now and again, so I suppose this does depend on the importance one assigns to that. If it's "one is too many, and how often it happens matters less than that it happens at all", then sure, and I hear that, but, just saying that this isn't something that can completely go away.
Going at this from the other side - is there a setting to turn the ship explosion radius or ship explosion damage off? I only find this fun when I happen to catch two unshielded enemies close to each other, and I would gladly forgo that little bit of candy for having "safe" phase ships of my own.
You could write a script that does what the ReducedExplosion hullmod does, but for all ships. (It would be a pretty simple one, though further discussion of that specifically ought to go into Modding.)