Would black garlic compliment or ruin carmelized onions?

Haven't tried it but I don't see that it would ruin caramelized onions. It might be rather good since both are so sweet and 'caramel-y'. Give it a try and let us know.

For alliums, I prefer to keep them separate rather than combining several to make a muddled, indistinct mishmash of similar flavors.

But do what you want. After all, whatever dish you put on the table should appeal to you (and your table guests), not to me. If you like the combined flavor, go for it.