Thanks for explaining your views on how TNG-tech would be applied to the older ball-turret phasers; after thinking it through some more, I do think this is the best explanation for what we've seen.
The notion of phaser banks vs. phaser emitters is a problematic one. Here's a crazy idea: what if there's something special about phaser power? What if the energy that powers the phasers is drawn off the main power grid, and then converted and stored in the ship's actual phaser banks, which are basically phaser "batteries" (in the electrical sense.) The energy has to be pre-phased or something to charge the phaser banks, but can be de-phased and re-routed back into the main power systems in a pinch. Then, the energy is phased again as it is passed through the emitters. As crazy as it sounds, this might solve a few of the problems we've seen. It might even explain those phaser power cells from DS9.
The DS9 TM's section on the Defiant actually describes the pulse phasers operating a principle kind of like this - they're designed to let the charge build up for a few seconds in the emitter chamber before being released, resulted in the pulsed effect compared to a standard beam. This creates more raw damage on impact, but at the cost of a shorter effective range because the pulse disperses quicker than a beam does.
Slight tangent, what do you make of the "megaphasers" on the Miranda? I had contemplated at one point making the things on the Excelsior's interhull the same thing, especially considering how close they are to the intermix chamber.
Going from the two main sources I know of for designs mounting megaphasers (Mastercom and Jackill), my general impression is that they're a heavier model of phaser than the bank-mounted units and are often employed either to give heavier punch in place of torpedoes (as on Mastercom's Daran
class fast frigates) or to supplement conventional weapons for tactical purposes (as on Jackill's Hellion
class heavy destroyers).