Reference software patch in paper
Yes, it is common and fairly reasonable.

So say you've implemented a new method for X.
And you submitted it as a PR on say github, as a new feature for 
"SuperXdoerLibrary", and it was accepted.
Then you would, say something at the end of the Section where you describe your algorithm something like:


  This method for doing X is now available in SuperXdoerLibrary (V1.23)1.


And then in a footnote put a link to the SuperXdoerLibrary website, or github page. And probably also put a link on your website

It is very common to refer to what implementations of your algorithm referred to in your paper. And a "good thing".

As to if it is a stand alone implementation, or as a component in a larger library, I don't think it matters.
I would in-fact suggest it is even better if it is in a larger library as that will generally mean it is in a more usable state.