As of BBEdit 13.1, the HTML Tidy built-ins are back and you should use those instead. This gist is so old it refers to "OS X", c’mon!
If for some reason you are using this, note @ryanfrancesconi’s comment about the correct place to put the file when using sandboxed versions of BBEdit.
The difference is lack of control over how white space is handled... I don't know if tidy has some options that I haven't seen? I like that you can setup the lint to be however you want. I really only use it for quick syntax checks.