After seeing so many variations of ships and the concept of a 'refit' being literally anything these days post Picard and Disco, it seems perfectly okay and reasonable that there are Sovereigns that don't really look alike. Exclsiors and Excelsior Refits existed together, and are now joined by Excelsior II's which aren't even refits but look like them so who knows? No reason why the Enterprise-E couldn't have a very unique refit.
That said, the ship in the MSD doesn't really strike me as a Sovereign refit. I'm really glad it doesn't seem to be that Verity class, definitely NOT a fan of it or the STO Enterprise-F. Profile of that ship is ridiculous looking to me.