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They can be very different, for example, the Kree's in the Ultimate universe are VASTLY different than the Kree of Earth-616. Ditto for beings like Gah Lak Tus and Galactus. Earth-9997 (Earth X) Has some very radical ideas about various alien races that vastly differ from the cannon Marvel Universe. So short answer: Yes, yes they can.
Adding, I guess that the Ultimate version of the Shi'ars is the most extreme example, since these Shi'ars are not even aliens at all, but members of some kind of underground sect.