I think Hamilton would better be suited under something like a "Best Live Performance" category, which would include other concert films (such as Taylor Swift's Folklore thing on Disney+). However, with 2020 having a weak slate of films, I get it. The person who probably biggest deserves a nomination for this didn't get one though, and that's Thomas Kail for directing this and really bringing the stage version to life in a cinematic way.
I get why Leslie Odom Jr. wasn't nominated as he probably would've been nominated for Best Supporting Actor and he got nominated for Best supporting Actor for One Night in Miami. If he was nominated twice in the same category, it would've made it very hard for him to win as he would've been splitting the vote between himself whereas he has a pretty decent chance of winning for One Night in Miami.