Board Thread:Theories and Speculation/@comment-2165692-20170426120148/@comment-734582-20170427211800

Arbaaz009 wrote: Well remember pain could summon ultimate summoning animals because of his Rinnegan Judging by the animals, Pain's powers and the databook descriptions, Pain doesn't summon them from some special dimension. With Naraka he could've revived/restored any carcass into a usable state (like, uh, one of the carcasses in Obito's hidden base). With the Six Paths of Pain technique he likely added Rinnegan and rods in order to use them as an extension of his body.

So TLDR: Rinnegan doesn't summon animals from some special dimension.

Boruto summoned that creature and somehow broke some seal. Both the summoning itself and it's desummoning were nothing like any regular technique. We've seen Boruto come in contact with Dark Chakra. We've seen that summon contracts can be made with anything as long as you have information (even souls or exotic spirit beings). So it's likely that in stead of making a useless summon contract with a snake, he made a summon contract with that beast in stead.