There isn’t a hard rule. Sometimes the Marvel omnis use the original art for the mass-market version, sometimes for the DM version. It depends on which edition (and printing) of which omnibus it is.
(And some don’t have variants at all, and some have more than two.)
Often when omnis have been reprinted (and the original-art variant was hard to come by in the first printing), the original art is used for the regular cover of the second printing. So it may be that if that Thor omni ever gets a reprint, we’ll see the original art as the regular cover.