It is beneficial to do the mods after break-in when you can use them.
But, during the break-in period, you should be riding the bike very mildly, so it won't matter.
If you do the break-in correctly, the stock equipment will serve you just fine during that period.
I know that it's hard not to be impatient, but there's no need for performance mods if you can't do any performance riding yet. It just would tempt you all the more to break the rules for break-in.
So, for these reasons, much like the posters before me said, leave the normal stuff in place until you have the engine broken-in enough to use the stuff.
Yes, they are good mods to do. After it's broken-in.