SharePoint Sites Best Practice - Project

I was referring to the Project Sites that get created for each project (if the option is selected) in an EPT. What you are referring to is adding a PWA instance to a SharePoint Site Collection and that's what is referenced in the URL you mentioned. In the former case when designing a Project Site template you can switch Web parts to use modern or classic, and these options are retined when saving the Project Site template. Within a PWA instance you may have many different types of projects and you can have a different project site look and feel (defined by the project site template associated with the EPT for that type of project). I would look up "Enterprise Project Types" and "Project Site Template creation" as there's plenty of existing material out there on these topics.