There are three advantages to the "better method"

1) HandBrake uses the superior Lanczos resizing algorithm (if you are not resizing, then you should see no advantage)
2) HandBrake uses the superior Yadif deinterlacing method (if you are not deinterlacing, then you should see no advantage).
3) HandBrake uses the superior x264 codec (for h.264 format). If you encode to high bitrates (i.e. large file sizes), most people cannot see an improvement over MainConcept. However, at low bitrates, the improvement can be dramatic. see: http://www.jazzythedog.com/testing/DNxHD/hd-guide.aspx#LBR

...Jerry (Jazzy's dad, however musicvid is the true authority on the "better" method. Nick Hope is the authority on the "best" method)