Very few concepts in general can truly be outside of the Omniverse; as the name itself implies the complete totality of all verses, as well as countless realms, dimensions, spaces, voids, etc. However, for Omnipotent beings like Creator, Destroyer and Hyperman, this is just another concept below their level.
Being omnipotent^1 allows these entities to be beyond the very concept of existence. This allows Godverses to be outside the limits (what few there are) of the Omniverse. Nonetheless, Godverses can still be classified as "existing", but the inner working of such a magnificent space are beyond any known level of comprehension within the Omniverse. If anything were to exist within the Godverses, it would be completely alien to every form of existence known and experienced within the Omniverse. Currently only the nature of Hyperman's Godverse is known by some inhabitants of the Omniverse, however even this knowledge is simply vague, abstract details as its true nature is almost certainly beyond their comprehension.
All three Godverses alongside the Omniverse exist within an even larger -verse known as The Barrel. (Our local Monocosm.) Between the Godverses and Omniverses is a void named The Outside, which encompasses the absence of existence. All of this, however, is of course still kept within a much larger structure known as The Box.