Hello,
On the matter of RTA timing: I'd agree all cutscene time duration (whether you skip it or not) should be included in that, especially with DtP 1-1 and 2-2 where timing the skip is actual cycle-manipulation (-> the stage parts in DtP are already loaded when the in-game cutscene starts and all the enemy cycles are started, so in a strict sense the run already starts with the cutscene). In my understanding RTA for this game is really just an informative measure and it heavily depends on loading times so it's not really comparable between platforms. It's a shame Bamco did not include time-attack mode for stages (at least they could've made the hundredth-seconds visible on the timer)...
Anyway another thing I want to mention is about IGT time calculation for IL runs: as I understand now, the time is determined by simply decrementing the start time from the end time. This by definition means the IGT is rounded DOWN to the final second. However the game does actually keep the in-game time in hundredth-seconds, so if you start the stage near the boundary of the next second, you'll "lose" the remaining part of that second. What I did to circumvent this is to try and pause the game right at the switch of a second, and create a save point there. It's extremely tedious, but should give the most precise timing for IL runs (that is if we continue using the in-game timer as the measure).