I believe the ultimate nomination is up to the voters, but the shows production and the actors push for a specific category. Example:
And category is definitely something that is gamed. For example, if there’s a “definitely will win” person going for say, lead actor, they might say someone is a supporting actor to try and win that category. Or if a production company has two comedy-dramas they want to win, they might push one as a comedy and one as a drama.
I can’t find a cite but I read something about actor vs supporting actor has to do with the number of episodes in which the actor appears. The context was that they killed off Michael Mando’s character off after so few episodes so that they could run him as supporting actor where he would have a better chance.
But as already mentioned earlier, the overall quality of the show theoretically shouldn’t matter for the Best Actor/Actress categories.
It is up to the performer to make the decision which category to enter.
Seehorn was also nominated this year for Outstanding Actress In A Short Form Comedy or Drama Series for a show called Cooper’s Bar (she lost), so maybe politics, gamesmanship, tradition or something else precluded her from entering as a lead for BCS.