There is a way to reset IGT, and keep all your chapters. It can be used to track IGT in Chapter Select without math.

1. Load or start the game with a complete save file.
2. Start something from Chapter Select (not continue).
3. Choose not to save.
4. When the game loads, quit to Main Menu.
5. Start something from Encounter Select.
6. As it finishes loading, pause immediately.
7. Quit to Main Menu.

At this point you can start any chapter from Chapter Select and run it with the IGT. If you do not create a save file, then you can reset the timer using Encounter Select when you start a new run. If you do create a save file, you'll have to perform all the steps again to reset the timer.

Unfortunately, I haven't found a way to create a save file with a 0:00 IGT to start with. You'll have to perform all the steps again when you start the game fresh. It only took me about 2 minutes of setup to be able to start running chapters.

If not used for a chapter leaderboard, it is at least helpful for practicing a chapter.