Are you saying you forced an oversize pin through the flash hole? If so, you may have pushed the web around the hole down into the primer pocket. Running it through a primer pocket swager could straighten that out.
Lapua and others claim the smaller flash hole makes for better accuracy by improving ignition consistency, though I've seen one study show a fatter hole did better with some components. So, you could also ignore the matter and just see how it shoots for you.