Hey, I'm new to this game but I just did some timing that may help with the IGT vs RTA discussion.
I looked at both of these runs, pulled each stage completion time and put them together in a spreadsheet. I believe the game starts the level time when the balls come out of the chute and ends when the last ball is cleared (clearly). If you take any level and time it manually, you get should get the given level time. I'm not sure how the game rounds, it could be the standard convention (X.5 or greater rounds up, else round down), or it always takes the ceiling (a 30.1 rounds to 31). I timed the bosses in a similar manner, but the level ends when the boss takes the last hit (or the last flame goes out in Zhaka Mu 1).
Using this timing method, I found that the first run you gave exactly matches the given IGT. The second run is off by 13 seconds. However, in your second run, you use a new file which gives you a cut scene that lasts about 13 seconds, so the difference may be because of the new file start.
Here's a google doc link to the spreadsheet: https://docs.google.com/spreadsheets/d/1NCU71II50j9xXzSZhX12F1n8BrNHrkAQ2kgL9BYgDqs/edit?usp=sharing
Hope this helps.
I didn't say that the timing method I used is what the game used. I'm saying I have found a timing that ended up being exactly equal to what the in game timer shows. It's good evidence that's how the game is timing. I was trying to provide some "data" as you put it:
"Changing over to IGT with no data on whether or not it was viable was also dumb"
On the other hand, you're using the argument that you have a hunch the IGT "likely" works off system cycles which makes it inaccurate. Do you have more evidence? I'm not on either side of this argument. I'm not an enemy here, just trying to provide some data.
I do think it's funny the IGT shows 4 hours for a run that was 1:25 IGT. THAT would be a good reason why IGT is not accurate. Not some hunch on how you THINK it works. It could also be the way you started the adventure mode, who knows. We need "data" as you put it.