They got Colin Farrell for the Penguin and made him unrecognizable. They could easily have Farrell play a different character in that Batman universe at some later point.
I imagine if Dormammu ever faced of against Wong or Magik or Daimon Hellstrom they'd still have Cumberbatch playing Dormammu without ever referencing that he sounds similar to Strange.
Doctor Who just cast two people who already had notable roles in the show as new characters to be the leads in a new spin-off. And they've even had actors who already were in the show become the Doctor later on.
If they truly believe that RDJ can pull off the acting required for Doom, then they might just have cast him for that, combined with the audience and media reaction that RDJ returning to the MCU brings, without the intention to make the characters related in-universe. Sure, having your heroes deal with an evil Iron Man is one way you could go, but it is definitely not the only one. I think either way casting RDJ in this role was a bad choice, but I think if they can have RDJ briefly show up in F4 and be completely unlike Tony then they could convince the audience that he was a good pick for this role and get away with it.
I mean, we already had actors doubling several times such as Minn-Erva and Sersi or Aleta Ogord and Ying Nan. And due to the Netflix stuff we already have Ben Grimm looking identical to Punisher's ally David "Micro" Lieberman, and will have things like Blade looking identical to Cottonmouth.