They would have to make some major changes NOT to mention the pre-catacylismic Atlantis, i.e. not mention the Deviants and the return of the Celestials. But I'd be very surprised if they did anything with Namor. They've got too many characters in that movie as it is.
And who would have thought that Black Knight would make it to the big screen before Namor???
Yes, the MCU is different from the MU -- though I'm sure there's one universe in the Multiverse that is just like the comics. ;p