ZB, I don't have a MNPV3 but I do have the MNPV6 and checked it for the clearance, it is about the same above the handle as it appears you have below the handles using the enclosure sides as a guide. My lid does rest on the sides when closed so I would think your handles would hit the lid, is that the case? From what I see the combiners should be the same except for the physical size but I may be wrong.
On my combiner it has an isolation material on the upper half of the box bottom but cut out for the din rail (
just wondering if yours is the same or as seen in the instruction manual just under and up the side of the PV bus bar) Maybe the material didn't get removed from under the din rail? WOW I should have looked better!
The material would be just thick enough to lift the rail and breakers to that height I would think.