I don't think even Warner Bros. know that

They know what movies they have planned and they definitely divide up characters based on what they have on the slate and in development.
It's been rumored that they originally wanted to do Gotham City Sirens but Matt Reeves had dibs on those characters--so they went to BoP.
So, yes, we do know that Orphan wasn't going to be in anything (as I said, any time soon, maybe several years from now something would've popped up--but the character was available because it wasn't in use elsewhere).

People would immediately be able to tell Phoenix Joker and Leto Joker are completely separate entities

Go look at any thread about the movie from when it was announced/prior to the release of material and the top comments are almost always about how confusing it'd be for the audience. Almost no one would confuse the pickpocket girl from this movie for a completely different woman playing a completely different character. Hell, ask anyone who doesn't know much about the comics what the character's name was in BoP and I'll bet you money that most won't even remember.
So, no, that's not an issue.

Obviously we can't verify OP's claim of opportunity cost

Not with 100% accuracy, no, but we do know that no one was fighting to put Orphan in a movie--the BoP movie was fast tracked due to Robbie/Quinn's popularity so they had to work with what characters were left on the table. Cain was one of them.
They may not have the long term plans they once did for DC but they also aren't completely ignoring the future--movies are planned in advance and characters are divided up in certain ways.

You're saying it can't be compared because the other characters are more iconic but, if anything, that makes it even easier to change the actress especially since this portrayal hasn't been iconic, either.

If you want to talk about opportunity cost then maybe talk about Black Mask because, at least, that's a character that had a good chance at showing up in the future in the Batman films.