I don't know if this translates to film or movies, but I worked at Activision back when we had the Marvel liscence. So a couple of things...
When we tried to make Marvel Ultimate Aliance we could not initially use Hulk cause Universal had his liscence, but the liscence was not just for the character but for all characters under his umbrella. This meant She-Hulk was unusable as well despite also being a member of the Fantastic 4 which we did have the liscence to. Silver Surfer was not treated as a seperate entity either, we could use him merely by having the rights to fan-4, just like we had venom and scarlet spidey, cosmic spidey, etc simply by having the Spiderman liscence. It covered all things spidey. Thats why eventually we started doing Spidey 2099 and other variants in the Spiderman games. The only thing we were specifically denied was Firestar. We had the X-Men and Spiderman liscence, but for some reason (likely tv related) she was on the list of people we couldn't use same as Hulk and Punisher who we just didn't own. So I don't know if sony actually has the venom liscence, or Fox has cable/wolverine/magento etc. I thnk that them having Spiderman/X-Men gives them the gauntlet of characters that fall under that umbrella. At least thats how it seemed to work for us.
But again, my insight is only from the gaming liscence, so movies may work different.
Also, there were 2 or 3 characters we had no choice in using. Marvel wanted them in the game. Thats why you ended up with ppl like Moon Knight being promenently featured when Namor is unplayable.