Phase frigates are bomber flagships.
Harbinger is a bomber flagship (bigger, easier-to-use AMB Afflictor) out-of-the-box, but with skills (Helmsmanship, elite Phase Mastery, Systems Expertise) it can become a brawler (phase, QD, lance repeatedly from medium range in quick succession).
Doom and Ziggurat are brawlers. Doom nukes things with mines, and maybe getting more shots in while enemy is distracted. Ziggurat paralyzes and locks things down with unblockable EMP motes while pounding them with plasma cannons and kinetics.
Not fond of bomber flagships for AI because they cannot use them effectively in that role.
I missed 0.7.1a and earlier releases with the no time-shift, no cooldown for phase frigates. They were brawlers back then, and the AI could use them well. Afflictor being super Lasher with autocannons and LAGs, and Shade being super Monitor. Now, phase frigates (and unskilled Harbinger) are bombers specially made for flagship use because the AI cannot pull off the delicate tricks the player can do.