Thank you for the question.
In PHP Tools we use IIS api which by default uses config from C:\Users[YOUR_USER]\Documents\IISExpress\config\applicationhost.config . You should be able to find site there. If you cannot find it there, make sure you are looking at the correct user, because you might be running elevated VS process.
However in the future versions we are looking into changing this, so config would be in .vs file which is the newer convention in VS.
Anyway any project specific settings (e.g. rewriting rules) should be included in web.config located in your project folder. IIS and IISExpress uses merged global and local configs together.
Please let me know if you'd have any other question.