Yes, it's strange.
YES, the "wild" part of "wilderness" means the same thing as the word "wild," but "wilderness" has a short "i" like "will" and "wild" has a long "i" like "why." And here's another puzzle: there is a perfectly good word, "wildness," that uses the long "i" like "why."
"-derness" doesn't have a meaning. "-ness" has a sort of meaning but I can't explain it.
I'm not enough of a scholar to tell you the history or background behind the words, but I can give you at least one other examples of a similar construction:
"The hinterlands" (short i) are remote regions, far from towns, regions that are _behind_ (long i) the populated areas.
Also, "yonder" means that big vague area way off in the distance over there. I almost have to wave my arm when I say that! It is related to the words "yon" and "beyond." No pronunciation difference, no "-ness," but there's that same "-er" suffix.