I suspect the answer would be found in the history of the word and that in, e.g., wild the i was long and, before the great vowel shift, would have been pronounced weeld. In wilderness it was short. Only long vowels underwent the great vowel shift so the pronunciation of i in wild would have gone from ee to eye and the i in wilderness would not have.

Just a guess, mind, but perhaps someone (nuncle?) would have the resources to check it out.