Yes, beam frigates and beam turrets actually use very different mechanics, and both mechanics were intentional when those units were implemented. After we added the turrets (several months after the frigates) I thought about going back and modifying the frigates to use the new one invented for the turrets, but I've decided against that at least for now. The major concern is that the turret mechanic can be significantly higher in cpu usage, which is ok for low-cap units but not so much for fleet units.
Also, I don't think it's a bad thing to have two separate types of beam weapon, one being the brute force massive wall of energy that smashes its way through a formation until it just runs out of strength, and the other being a sort of energy field intensifier ("heat beam") that just makes life very uncomfortable along that line.
One thing I do want to do is have the beam frigate draw the line through to maximum range, to reduce the gap between its "average usefulness" and it's "max usefulness" which can currently only be achieved by intense micro. Of course, there will always be a large gap on line-aoe stuff unless we have the autotargeting analyze (at the time of firing) all possible targets for maximum targets on the line, which would grind even the most powerful consumer machine to a crawl in one of those 2000 vs 2000 fleet battles.
And to clarify about the turret's mechanic: each beam (higher mark turrets fire multiple beams per salvo) starts with the listed strength; it hits the first target in its path (whereas the beam frigate always hits the specified target, the others are just in the wrong place at the wrong time), and applies its damage. If the target survives, that's it for that beam. If the target dies, the beam strength is reduced by the damage done (scaled by bonuses) and continues to the next target on the line (if any), and repeats the check. This allows a beam to one-shot say 3 bombers in a row without being able to one-shot an arbitrary amount that happened to be on the line like a hypothetical super-powered beam frigate would be able to do.