I did a run with Cabbage Corp + Drake + SM&M++ today with the level 10 plasma Kuma repeater and Drake WMD launcher as my endgame weapons.
That gun performs very well against the Phobos. It's not just that it's level 10; because it's a matter repeater with some inaccuracy, the Phobos wasn't able to get any APA shots through that screen of fire. I engaged it at close range and kept the front of my ship pointed at the Phobos as it went around me. After less than a minute, its weapons were damaged, and the fight was basically over.
It felt about the same as engaging the more advanced Manticores in the arena with a Moskva repeater and Stilettos.
Again, I suspect that if we just had a greater variety of weapons in the late game, it would be much easier to play without having to engage enemies at a distance.