There's something of a US/UK usage split regarding the plurality of nouns. For example, companies, public bodies, and couples / pairs are nearly always singular in AmE, but BrE is often very flexible in this area.
Here's an example matching OP's cited usage which seems okay to me as a Brit, but apparently not everyone would accept it...
Our commonality and difference is sustained by apostolic truth and the promise of the unity of all things in the worship of God
At least with that example, I have no particular objection to using are instead of is. But that's certainly not the case with this example...
In a logical sense, similarity and difference is a binary relation in which similarity excludes difference, and vice versa
...where the entire sentence falls apart if you try to change is to are. I'm just glad that as a Brit I don't have to let things like that bother me!
It may be an inviolable rule1 in AmE that "commonality and difference" must always be syntactically plural in AmE, but that's not true of British English.
No-one could object to The commonalities and differences are unclear, but for the exact version as presented here, I personally prefer the singular verb form. And I very much doubt the writer would accept that he made a "mistake".
1 Obviously even in AmE it's not an inviolable rule. I'm deliberately exaggerating the scope of a "general principle" that I think is slavishly applied far too often in AmE.