Is the FCOM the right vehicle for limitations - shouldn't there be an AFM to be the definitive source?
My own guess at the apparent discrepancy comes from inferring the intent of that "special operations/flight with landing gear down" bit - which sounds like the case where you conduct an entire flight gear down (ferry to maintenance with a gear problem, say).
IF that's the case then there may be fatigue issues restricting your gear down speed for an extended period, whereas the VLE is for "normal ops" of only a few minutes with gear down, and so the fatigue issue is smaller and already factored into your inspections and such.
In other words its safe to fly at VLE with gear extended - but maybe not for two hours.