I assumed so, as I made sure to pause the timer when the window popped up, to make it clear I wasn't doing anything else while thinking. In my opinion, it should be just fine, cuz if you aren't doing anything else while the timer is paused, it's like having figured it out beforehand (Which I should have done lol)
My 16th attempt at the full run since the new record I used my own splits with the first mission, followed by Shadow projects and then the end. Got rather unlucky with the UFO which stole about 5 minutes from me, and messed up a turn on the final mission costing me another 4. Definitely didnt get the best possible run here, and there is still wiggle room, especially if you can get a scientist as the first drop. For now though, my pain is over, and I will gladly leave it to anyone else unhinged enough.
Warning for headphone users: Every cutscene + 2:33:55 for I am very loud when celebrating.