Reasons - fine.
Why I wanted to see such a system as i saw in the concept art would be purely because that's exactly how I imagined phase ships to work in my mind once they where announced in-offically. I always thought of phase ships to be working and acting a lot like todays submarines, or even the old submarines. That they'd be semi-transparent for the friendly side, but be nearly invisible for the enemy, short of an alpha transparency of, say 10? Because old WWII submarines could either be detected by the use of sonar, or of they where close enough to the surface and you had some men with great eyes onboard, you could track them through the air bubbles the engines let out. In fact, this was the main way of tracking torpedoes once a submarine has launched them. But the main reasoning for this is that this system was what I purely had imagined when i heard the word "phase", logic being that they'd be so far onto the other dimension that they'd be nigh impossible to see, short of looking real good, and noticing any minor movement. The Ai would have to be dumbed down in this matter, to prevent it from detecting the phase ships. How this would be done I have no clue to, someone else can come up with it.
But the system you are going to put in place right now felt a little... Awkward and not exactly as i expected it, even though It's for balance.
TL;DR: gut reaction based on logical information on todays subs.