What boundaries? You mean the boundaries you made for the game yourself. I don't recall reading that Kojima has ever set any boundaries for the series. If it bothers you that much just think of the Wormholes as supernatural instead of technology since you seem fine with accepting supernatural elements!I can understand thinking the worm hole is overboard, but your reasoning doesn't really jive well. Everything Mantis does is still physically impossible. Vamp running on water and up the side of a building is still impossible. Fortune deflecting missiles even after her tech is disabled is impossible. I think it's really just that the wormhole falls outside of the boundaries the MGS universe has created. It has people with supernatural abilities, and technology that is a few decades ahead of its time. However, it doesn't have futurama-level space scifi with worm holes. It falls outside the game's universe feel.
I find it a bit ridiculous because I think it'll break the illusion a bit every time I have to use that thing indoors later in the game. I'm not really annoyed by it though.
Or you know, don't use them. Cause you don't have to.