My guess would be its the rudders, and that either the backups aren't as capable (not as much flow rate, or don't pick up the demand instantly when 1 or 4 fail) or have never been demonstrated and so Boeing are conservatively assuming there may be some degradation in capability and adjusting VMCG accordingly.
I very much doubt they repeated VMCG for an MEL dispatch case, so chances are it is an analytical penalty, and when you do it that way the tendency is to be a bit more conservative so as to err on the side of safety.