Two things: I don't think exposure compensation works as well with spot metering because that metering, by definition, is isolated to a very small area. If you are metering what you want to be exposed correctly (example -- a spot-lighted face on a stage with a dark background) then the overall scene may appear to be under exposed on your LCD and in the histogram. But the face will be correctly exposed for detail if you enlarge it and examine it.) Matrix and center-weighted metering on the other hand, are alread trying to compensate for a variety of scene brightnesses.
And that goes to your interesting comment that you have more difficulty in brightly lit summer scenes. I have not been to Malta, but I have worked close to the equator in Africa and the mideast, and for sure -- it is bright there; maybe brighter and contrastier than Nikon envisioned in developin the algorithms that manage center and matrix metering. You sure don't have much of a so-called softly lit "golden hour" at those latitudes.
I'm not an engineer -- I'm an old photographer who has shot from dark room days 50 years ago to my D700 bodies today. I think you are just dealing with lighting that a large percentage of us never see -- and if you have to tell your camera to lower exposure to get what YOU want, I'd be comfortable doing so. Good shooting with you Nikons!