For starters, I don't speedrun, nor have I watching any of the R&C 2016 speedruns, nor do I know if the speedrunning scene is popular for this at all, but I found a glitch that may or may not be helpful. On Pokitaru, after destroying the hydroharvester ships, I died as the mission was fading out into the cutscene. The game went to the loading screen then played the cutscene for after you finished the mission, and when I regained control of Ratchet, as long as I was in the main hub of Pokitaru (i.e. not the pumping station), I could no longer swim, instead I would fall through the water to the ground and walk on the ocean floor. However, the mission was not labeled as completed, and flying back to the world loaded me back into the mission with me only having to destroy one more of the hydroharvesters. After doing so, I lost the glitch.

Like I said, I don't know if this is helpful at all, but I figured I'd share it in hopes it may help lower run times or something :)