Is co-existing with the skunk impossible? They eat a lot of rodents and bugs and become accustomed to seeing people so getting sprayed is not likely.

Where are they denning? There are no repellents that will work unless you have them so strong they are annoying to you. You need to get serious about putting a hardware cloth barrier all the way around the buildings instead of worrying about each entrance as the skunks find them.
They are out of the den during the dusk/night/dawn hours mostly ... except that if they are breeding, there will be babies in there all the time.

1 - Find and seal ALL possible entrances except the one you mentioned.

2 - Watch that entrance in the evening until you see the skunk leaving.

3 - Block it with something heavy that can't be dug under or wiggled around.