Yeah, it's still borked. It's a bit concerning that this isn't being addressed, but I guess a lot of attention has probably been on fixing the upgrade system for Holodeck...
Just played through the mission post-patch, and there were still two Coopers in the final cutscene. Since this was listed as fixed in the patch notes, it might be worth looking into.
The fact that there's basically no cooldown on the Vaadwaur battleship's DESTROY EVERYTHING weapon is pretty annoying... Is that thing on a 270 degree firing arc, also?!