Only .htaccess support is missing from nginx. Good web server.
While it is a performance and security burden, people reject .htaccess is too readily. It has enabled users who aren't quite programmers to assemble sites out of web applications and components that live in different subdirectories. It has clear value. (Not that I think nginx should implement it.)
In that case you would still need some way to trigger a reload of the htaccess, right?
If so, is there a usability difference to just including nginx configs on the same locations?
It doesn't need to, though.
These days you only need .htaccess for compatibility with old PHP apps. Stacking another instance of Apache on top feels bloated.