I don't think that I agree with this at all. If anything, the relationship and understanding they formed in that era went a long way to disprove those "differences" translating to them not being able to be together. If anything, we saw that it was because of exactly who they were that led to them having the deepest and most meaningful connection with one another than they had with anyone else. It is that established friendship and connection that propelled their union in Kingdom Come. What we saw was that it wasn't that they were too different to make it work when they first met, but that emotionally, maturity, and experience wise, they just were not yet ready for the kind of relationship which they could have and deserved. And it was that friendship, that relationship of deep trust, honesty, love, transparency, dependability, vulnerability, the give and take, and many other qualifiers that they established that would eventually make any romantic relationship between them extremely successful.
When the friendship was destroyed under questionable circumstances, for Diana to be forsaken by the one man (Clark) who basically knew her better than anyone else to no longer stand by her, it was by a writer(s) who wanted to push another narrative and insert another relationship.
I can never buy the claim of Superman and Wonder Woman being too different. It just rings completely false and hollow. When the very inspiration of her creation is connected to Superman it just sounds like a very ridiculous excuse. Sorry, but I hate that fake argument from detractors because it usually lends to unfavorable mischaracterization of Diana.