Hmm, it was integrated in the same way that adaptive formatting was, in that beautifying selections, alias expansion etc take AF and the .editorconfig into account. But when you beautify the whole file, just the profile is used without input from AF or .editorconfig.
For adaptive formatting we do that because it allows you to fix files with inconsistent formatting that are confusing AF, without having to turn AF off, beautify to get it into shape, and then turn AF back on.
It might not make as much sense to do this with .editorconfig, since either you want to use the editorconfig settings or you don't. There isn't a third "confused" state to worry about. I need to look into this more.
In the meantime, the only workaround I know of is to do a select-all and beautify - even though it's the entire file, the selection will make it pull in editorconfig changes.