They don't affect plugins directly, but for example there is a flag which allows you to force GPU-accelerated rendering on unsupported system configurations, which PPAPI Flash could take advantage of. It's indirect control. Flags & browser settings don't control plugins, but through them you can change what PPAPI plugins have access to.
And to the other post, yes, if your Flash, drivers, and browser are up to date, PPAPI Flash should support hardware acceleration. You might run into problems, like for example the newest stable version of my graphics driver broke GPU-accelerated video decoding, so I'm using the beta driver.