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.

Unfortunately, if you skip at different parts of a cutscene, you can save or lose more IGT than intended as it tries to add the remaining cutscene time, but fails to do so accurately by randomly overshooting or undershooting that calculation.
Even if you simply watch a full cutscene you'll probably get a different IGT result than if you had immediately skipped it. An example of this is the game's intro cutscene where if you immediately skip, you'll get a 3:44 IGT, but if you let it play all the way through, you get 3:27, and if you skip somewhere near the end you can get strange results like 3:25 or 3:28.
^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.