The Gym leader will not have to go through the usual norms as a Pokemon trainer, they can go directly to the league and challenge whenever they want.
My proof here is going to be Volkner from DPP:
>All right, I've decided! If I find you to be weak, I'm going to challenge the Pokémon League.
But he's also said to be the top Gym leader in all of Sinnoh, so it's a reasonable theory that he has all the authority to go directly to the league, but in Pokemon origins, it is shown that Brock deliberately uses his weaker Pokemon against Red, as per his gym badges to match his strength, which means it's highly likely that if they had battled later, he would've used something else, meaning that all Gym leaders have about equal strength, atleast in levels.
Also Gym leaders are directly promoted by the league, which means they are acknowledged strong trainers, and have all the right to challenge the league, as long as it does not disturb their position as a Gym leader
Source: Some bit of knowledge in the game, and this about Volkner.
Hope I helped!