5 minutes is slowish for 1080p on a modern computer. You could share server logs if you want.
Plex Transcoder is Plex’s version of ffmpeg with additional special sauce. You don’t need to specify -codec:v blah because ffmpeg will autodetect the codec. If autodetection doesn’t work, neither will specifying the codec. 
The quality/size/aspect flags stay the same when Plex generates VPTs.
You could adjust the FPS. That can significantly speed up VPT generation and reduce VPT file size. I should have suggested this before:
