Is there a tool to see every WordPress site that’s using a particular plugin?

I dont think Beyond Multisite is going to do it.

when you look at a site that is using Yoast you will see that it loads ‘yoast.js’

The best idea I have is to use a site like publicwww.com (free for first 3M pages) to provide a list of all sites that it knows also using that file.

https://publicwww.com/websites/yoast.js/

That link should work.

This may not be ALL the sites it is only the sites that the page has crawled / discovered.

There are prob other sites with this ability.

Hope this helps.

Cheers,