You might want to factor in a disruptor effect over time...even that could bump the transphasics higher on the dps scale.
From my own testing and parsing the results, a transphasic boat using disruptors can produce a respectable-enough result to make it worthy of at least running STFs with it. And hey, it is a completely different way of flying an escort, so there is that.
However, from my experience, even the Tac Cubes don't have a shield face up for long against my fleet teams, as it gets rooted and debuffed so bare hull is facing us pretty much the entire time. So if you're running with a pug, it might be fun to roll an advcort transphasic build for utility, but otherwise I think quantums will still be king if you want to maximize your damage. But again, if you're pulling 5-6k raw dps in your transphasic boat, I see no reason to change.