They wouldn't have to be recompiled. Unity apps running via UWP don't execute directly in the browser document context, UWP is it's own stand-alone plugin which

They wouldn't have to be recompiled. Unity apps running via UWP don't execute directly in the browser document context, UWP is it's own stand-alone plugin which is then embedded where needed in the page (similar to Flash and Java), this is why you have to download the UWP executable in addition to the browser plugin. The browser plugin is merely a wrapper for the UWP binary. Unity apps compiled against the UWP runtime should run all the same regardless of whether UWP is wrapped in an NPAPI or PPAPI plugin, unless the wrapper plugins themselves and/or how they call the UWP runtime are implemented differently.