I'll see how I go answering some of the questions.

So yes, Tonics are allowed in runs. And you can start the run with them already unlocked. As you know Tonic progression is carried over between global saves on your account, and to clear it you would have to uninstall the entire game, or do some backscreen work in Steam files. No thanks; so just have the ones you want unlocked before starting a run.

The IGT isn't exactly known. But we do know it runs during all cutscenes, even the final cutscene after Capital B's defeat. Menuing and loads, not too sure. However this is irrelevant because we do not use IGT as a measure here, it's too inaccurate.

When it comes to timing methods here; Console is using RTA. And PC is using RTA (temporarily) until we have a working Load-Removal script for Livesplit. So yeah, the IGT isn't necessary.

I'm quite interested in a 100% route. Any % runs aren't something I would like to do. I'm happy for any informations about that.