I'm a speedrun video viewer and I've noticed that two new lines added to the intro skip rules:

... Runs must not acquire and make use of Dragon Parts from Dinraal, Farosh and Naydra. Runs must not acquire and make use of Dragon Parts or the Master Sword from the Light Dragon until after the final Dragon Tear Memory #17 is collected.

Is this a restriction on the entire run or just the save file in the Room of Awakening?

If it's a restriction on the entire run, what's the justification? They are listed in the game rules, which means that Any% is also restricted.

Or if it's just a limitation on the save file, is there any chance to do this before creating the save file?

It's a restriction on what you're allowed to do during the run; however, no viable routes in the Any% category are affected by this. So it only really matters for longer categories like All Dungeons or All Shrines, where dragon parts might be used for cooking.

"If it's a restriction on the entire run, what's the justification?" This is key, if it doesn't affect the route, why is it banned at all? what is it trying to prevent why ban it at all?

if you use intro skip, the dragons flight route may be messed up, thus making it affect part of the game depending on wether or not you use intro skip, so they banned it as a "just in case" situation.

or at least thats my understanding

You're allowed to collect things from the dragons, as long as you don't use Intro Skip.

Quote https://www.speedrun.com/totk/forums/6xsfl#j08wd

So I get it.