I kinda understand what you're getting at.
If you know the file format inside out, then maybe you're right, it is quicker to type out a list of nodes in a file. However, the problem comes when you don't know the format, you make a mistake, or want to push the same permissions across multiple servers.
File parsing errors are far far harder to diagnose with a user, than commands. At least in LuckPerms, you literally cannot make errors when setting up permissions, as it won't let the command execute, and it will spit back an error explaining exactly what was wrong. I think you'd be lucky to get that much diagnostic when loading screwed up YAML.
Off-topic slightly, I was under the impression that Sponge wasn't really supporting YAML? Perhaps I'm mistaken, but I'm pretty sure the de-facto for config files is .conf here? Maybe not, Idk.
Anyway, back to your point. LuckPerms actually does have support for flatfile. User, group and track data is each saved within it's own file, in the popular json format. My advice is to generate a file for yourself, using commands, work out how the format works, and then edit the files by hand if you must.
I should also add, there is support for automatic migration from a number of existing plugins, GroupManager included. Check the wiki page for info on that.
That aside, thank you for the feedback!