As long as the writers are conscious of the risk, the problem will be avoided.
In any case, as others have said, the two characters are hardly identical, and there is little reason to suppose that the similarities they do share would lead to the plots being too similar. Obi Wan Kenobi and Gandalf are roughly the same character, but the movies in which they appear are quite different.
That said, I am not persuaded that Darkseid "needs" to appear in a DC movie. On a superficial reasoning, he does seem essential to the DCU as it appears in the comics, but that is really a product of their longevity and volume. The DCU now has so many characters with such a long history of interaction between them that it has developed a hierarchy of threat, which inevitably needs somebody to sit at the top. The movies won't have that, since all that they will ever be able to show is a tunnel drilled through the middle of the DCU trunk.
Personally, I don't find "ultimate threats" very interesting as fictional characters, since they lack vulnerability and therefore nuance. Add vulnerability and nuance, and they cease to be the "ultimate threat" and become an anti-hero: see Satan in Milton's Paradise Lost.
They are nothing alike.Not like Drakseid/Thanos
Seriously, it's a ****ing ridiculous notion.
