We now have the ability to upload changes to the Phantom X mod directly onto FAF without delay, which makes things a lot easier. This thread keeps track of current development goals and progress.
On of the biggest problems of Phantom games has always been the random assigment of teams. Unbalanced teams are frequent, and represent a much bigger balancing problem than any other issues.
As of today, a preliminary autobalancing algorithm is part of Phantom X. It can be deactivated with the appropriate lobby option. The script checks all players eco progress, and decides the assignments based on that.
Future version will include more randomization.