Handbrake is a pretty wonderful piece of software that has easy to figure out settings for ipods, ipads, appletv, etc.
It's probably tough for the Rifftrax folks to determine a balance between, "plug and play right after you download them" and "having a dozen different versions" of the same file to take into account all the different ways to play MP4s. Sure, people could use Handbrake, but then you will risk losing customers who dont want to go through all the time/hassle of file converting as not everyone knows how to do that.