Title. I don't understand how it is possible. Shouldn't it be the opposite ?

Cutscenes, even when skipped, will be counted towards IGT, but are not counted towards RTA. There is also the intro cutscene, which isn't "skipped" per se, but rather the game auto-saves after the intro and that save it what is used by runners when starting. If you go watch a run, you'll see the file selected for starting the run have 3:44 IGT already.

Ok, so like if a cutscene last 5 minutes and it is skipped, 5 minutes will just be added to the counter instantly ? That's... a bit weird.

Yup. My guess is that they didn't want whether or not you watch cutscenes to affect IGT since there are in-game rewards for meeting certain thresholds. They could have made cutscenes never count towards IGT, but meeting those thresholds might have been too easy. Just speculation though.

^Bug with emulator IGT pacing during cutscenes. It also rolls back on deaths/reloads, or pauses when there's any menus up. See more IGT info on the Discord server. (direct message link)

^ this is entirely false don't listen to this

^ this is completely true, heed those words!

What makes you say it's false? I streamed tons of IGT tests with a live IGT value displayed.

Redid a bunch of tests on 1.0.0 & 1.0.1 on both latest Ryujinx & Yuzu EA. The only corrections I'll make are the inconsistent times on the intro cutscene, and potentially remaining cutscene time over/undershooting, because both of these emulators have IGT pacing issues during the intro cutscene especially, and minor pacing issues in other cutscenes. Basically the IGT will randomly slow down for a moment, then go back to normal. It appears steady during normal gameplay. To summarize, skipping a cutscene VS watching it may result in the same time on consoles. I can't confirm this without a hacked console. That's pretty much it. The rest I posted here and on the server is still true. I'll edit out misleading info and add more clarifications.