I imagine it would be, as long as the game keeps running as a single segment? The rules sections need to be filled out for NG and NG+ as well.
Sure you can take as many breaks as needed but the game and timer keeps running. I myself took a couple of few minute breaks. Also i should fill out the rule section at some point.
I 100% agree with restroom/stretch breaks counting against the run's official time. I wonder if a sleep break (6-8 hours) can be accounted for on the overall runtime, while the "official run" is paused. Perhaps the timer can be paused at a save point, then resumed as soon as the file is reloaded.
Typically in long speedruns (think Baten Kaitos 100%, Pokemon Stadium, Metal Gear Solid V: The Phantom Pain 100%), the clock continues the whole duration of the run, otherwise it's not a 'single segment' run. What you are describing is a multisegment run.