It's not a superlative in the great majority of its uses, any more than "over" is in english in, for example, "overtake". It does have this sense, as you say, in some usages, such as "supernatural" = "übernaturlich", but it gets it in this case from being "above" or "over" the natural, and it's not applied this way uniformly. German uses "ultra-" just as english does in scientific terminology, for example. I think it's unquestionable that the "Uber-" prefix in english usage hinges completely on "Ubermensch".
I was thinking more of its use as a prefix for titles like “Ubersturmfuhrer” and “Uberleutnant.” In those examples, it means exactly what I decribed: “over” in the sense of “superior to” or “beyond.”