If we can accept Joker killing Batman's parents in 1989, we can accept..
Batman 89 and Spectre are similar in many ways: Bond\Batman goes after Blofeld\Joker, a criminal mastermind who runs an evil criminal organization, and later realizes that he has met this mastermind before as a child.
Furthermore, towards the end of Bond\Batman's pursuit, they both come to learn that Joker\Blofeld were the real authors of our hero's pain.
The film is always playing on Epix, and I always watch it. And for some reason, the idea that they were foster brothers doesn't bother me as much as I thought it would. Again it all goes back to that first teaser trailer: adoption papers, "It's been a long time", and it was fairly easy to put it all together.
Furthermore, these developments add an element of fate\Greek or Shakespearean tragedy to the proceedings, like it's all an inevitable dance to the death, for both movies.
I still think that the whole "This cuckoo made me realize my father's life had to end" is something that requires exposition\explanation, and can be done beautifully and masterfully with Waltz, similar to Silva's introduction in Skyfall with one super long speech in one single, crisp take, that explains our villain's motivation.