If I may raise my hand here, phase freighters are one of those concepts that's fairly volatile in the modiverse. I've tried to make one, and I had a bunch of people tell me it wasn't a good idea, and as it turned out they were right. A phase freighter, in the simplest sense it can be, is a tad broken because it's nigh impossible to catch, so suddenly all your fleet's cargo is 100% safe no matter what.
Not saying the idea is inherently bad! But it's a risky one, as other folks who've tried it will no doubt tell you. Definitely needs to be treated with caution.
Generally, if you're going to go with a phase freighter, you want its capacity to be very limited - good for a phase ship, perhaps even good for a warship, but rubbish compared to a good old civilian hauler. It has to be very specialized, in order to not be "the best" at its job.
(If you want a sneaky "spec ops" freighter or personnel carrier though, I'd just go with the Phase Field hullmod. It doesn't need a full-blown phase cloak to get the point across.)