The "maintain 1000ft" instruction was for a different helicopter that was just taking off from the grass. The "maintain 1000ft" instruction was not for the accident helicopter.
The Cirrus was instructed to report a midfield left downwind for 30 with three helicopters operating below him. Absent any other altitude instructions, this would constitute 1,300ft since that that is the TPA. Cirrus acknowledged this instruction.
Tower then immediately reported him in sight and instructed him to maintain his current altitude until base. This altitude should have been at least 1,300ft. The collision occurred immediately.
I'm having a hard time picturing the Cirrus being 300 below TPA that far out. Especially since he was at 1600 just prior. And I'm having a hard time picturing the controller not saying something about it if he was. Of course I'm guessing, but it is my best guess based on available facts.
What seems more likely, unfortunately, is the helicopter climbing too high. We now know it was a pilot on a check out flight, not an experienced local pilot or CFI. Which makes climbing too high in an unfamiliar traffic pattern a little more likely. Again, totally guessing.