So, I have found a replaceable glitch wherein by spamming up/enter and right after clicking "New Game" in the lag between the actual button press and the start of a new file, I can click either "Continue" or "God Mode" while still hitting the "New Game" button first and not exiting the game. Even if we determine that using continue while pressing new game shouldn't be allowed, "God Mode" starts a new file while leaving with 1hp and (more importantly) skipping the opening cutscene, which would save time. Finally, the opening cutscene itself is laggy for me while the rest of the game runs perfectly fine, and because of this lag I am fairly certain I lose a few seconds starting every run attempt.
With all this in mind, my proposed solution to the problems stated above is to change the ruleset to start the timer on the first frame Zigloton hits the ground in the opening room (as happens at precisely 31.10 in the current Any% WR). This solves any of the save profile and opening lag problems while still giving us an absolute metric by which to start the run. If it is preferred to start it a bit before that, another possibility is the first frame in which Zigloton is on screen (30.82 on the Any% WR), which only happens after the room is fully loaded. I prefer the solution with Zigloton hitting the ground because it is a bit easier to start the timer correctly when running, but ether way makes sense.
If this request is denied for any reason, I would ask that you look for another way of starting the run timer differently as to circumvent these problems, and sorry for the wall of text.
Glad to hear your concerns! Approved! Have fun :D