No idea, sorry...
Since this is just a non-fatal warning I will just ignore it. After reading a few posts about this "me_method" param my impression is that this global option was removed because each different encoder handles it differently. So there are now encoder specific options for motion estimation. After some user complaints the "me_method" param was reintroduced as an alias for the encoder specific option.
The warning probably means that this alias is not applicable for the MPEG2 encoder. IMO the worst thing which could happen is that the option is ignored and some default being used.
//EDIT/
I also updated my post #6 (removed the "sc_factor" param and reduced max bitrate from 8500 to 8000). This means of course that the average bitrate must be at least a little bit below 8000.