It is definitely a health to drop shot ratio I helped a mate do it and noticed the change cause back when I did mine we didn't even damage phogoth all we did was take him off his chains and head back to orbit after xyor was gone You don't get any extra reward for killing boss

I did the bounty last week and at first I thought there was a glitch as well because the ship was not spawning after the 2nd one. I was running around in the area with Phogoth and nothing was on the radar either as far as enemies other than the marker for Phogoth himself. So I thought I was going to have to start over. Then I ran over to the far side of the little arena (when you come in door to phogoth the right side far wall not left where rocks are) there were 2 wizards just chillin. Kind of odd because they didn't show on radar but after killing them the ship spawned. Took a good 5 minutes to actually see the 2 wizards and realize the ships were not glitched. So if your having trouble with the ships spawning, just look high and low in the arena area and make sure you have killed everything.