It is still possible to install militarized subsystems, install assault/escort package, smod the package, and then drop the militarized subsystems. Otherwise the increase in crew required is horrendous, and I expect the ship to die from time to time. So for Prometheus MK II, I could see maybe 2 tachyon lances, 2 HVDs, some sort of missile, and 2 fighters or bombers. With an officer, this would be 2x 1750 range or even 1950 range tachyon lances and other stuff for just 32 DP.
The 10 fuel/LY is awful though, regular Atlas/Prometheus are now 6 fuel/LY, but the MK IIs are still 10.
Speaking of Buffalos, I was testing out Buffalo Mk II's. They have horrid PPT (120), converted fighter bays without the reduced dmod skill really hurts fighter speed, and 2 fuel is a lot for a 4 dp ship. And the fighters barely engage, even when their parent ships are ordered to. They still close in to ~1000 range even if they have all harpoons/pilums and no other weapons, PD or otherwise.