I'll take a guess that the VLE statements occur in the normal part of the flight manual and that somewhere else, perhaps close by, is a statement to the effect that cruise is not to be conducted gear down.
While the VMO/MMO statement is from a part of the manual allowing the whole flight gear down?
So it may come down to:
fatigue load assumptions between being at VLE for a few minutes and being at VMO indefinitely
or
bird strike risks (exposure time again)
as two guesses