Thanks for the question! I admit it is a bit confusing, and that is in part a result of there not being a lot of interest in this game (except for two people), so there hasn't been a lot of motivation to keep it updated. One reason in favor of waiting until the player gets control is to help mitigate the burden of load times from the game for different system specs. If we allow pausing of the timer during load times anyways, there's little reason to start the timer before the player gets control of the first level, since at that point you're really only testing how good someone is at skipping (one) cutscene. A loadscreen auto-pause is somewhat in development, but had been put a bit on the backburner. I admit this isn't a great reason, and I'd love to continue discussing it with you to find a better solution/create a more structured system. With three people interested, I've taken the liberty of creating a discord for speedrunning this game and it's sequels. Feel free to access it here: https://discord.gg/Nr3kAZR6

Small thing I noticed when testing this out. It seems that since you avoid all opening cutscenes, time doesn't ever start, so (at least for me) its forever 5:15 am...