Yeah, that was the first thing I tried as I use it in v2 for similar reasons, but it wasn't having any of it.
More importantly, I can now do this:
/**
* @include 'components/alpha.js'
*/
And it will pull in the docblock from that file into the class it is currently processing, something not possible with jsdoc natively.
I'm also making use of some custom tags like @demo to inline a working Phaser example (sort of like @iframe can do in some versions). And have extended the @tutorial concept so you don't have to keep all the tutorials together in the docs repo, but can keep them external.
I'm a lot happier with the flexibility that using an existing parser and my own custom output is giving me.
Cheers,
Rich