Okay, after having watched several runs and verified a couple - start of all runs should start at the transition between the loading screen and inside the ship. While we could start it on the opening of the exit of the ship, it's harder to see in youtube frame by frame analysis.

Ending should always be the moment at which the white flash of the bullet hits the crystal sphere of Wormy's mouth for the last time. That frame is easy to spot on youtube frame by frame analysis.

Each boss timer ends at the same point as well.

Until an official implementation is made by Master Indie (which there are no known plans for one so far), the best suggestion I can make is start game at frame one of the hatch beginning to drop - it's easily doable for perfect timing by looking at the playback video. For now, we'll have to start and stop timers on our own. Afterwards, with each boss - the end timer occurs when the crystal turns black - there is an initial white flash - that first frame of the white flash with a confirmed black crystal could be the timer for the end of each boss with the exception of the worm.

While defeating wormy occurs at the black crystal moment, I feel that escaping him should be important to the run as well. Nothing bad happens without it, but I don't feel it complete until you do escape him. I'm not sure what could be called the exact end of him in that regard. He does start to explode and it could be considered that the first explosion is his death, and if you're still inside of him, you haven't succeeded, but again - how do we define "inside" of him. Perhaps for now, the actual runs end at the exact frame that the final spherical crystal is turned black (i.e. the white flash before the black).