RTF delineates paragraph elements with {\pard … \par}.
HTML delineates paragraph elements with
…
.
For an HTML paragraph element to appear in a Scrivener project, either the user would have to type it in, or an external tool that has access to the project would have to create it.
I imagine PWA channels into Scrivener projects through their underlying XML files. Even if you delete the paragraph element in PWA, it is probably being recreated when PWA closes the project and passes the text back to Scrivener.