I don't buy into any physical/physical "teleportation" theory because that's inconsistent with the level of technology portrayed within the series. The story does make reference to Schopenhauer's "The World as Will and Representation", thoughhttps://en.wikipedia.org/wiki/The_World_as_Will_and_Representation
(the book Chito picked up at the start of ch. 45, "Library"), which lends itself to a more metaphysical interpretation.
According to Schopenhauer, the entire world of percieved phenomena (time, space, causality etc.) is all merely the projection/representation of a singular will (the "will to life"). Human wills/consciousness themselves are also further shards/expressions of that will -- in the end we are all facets of a singular, unified phenomena that is the basis of all things.
In chapter 46 ("Silence"), Chito experiences the unification of her consciousness, first with Yuu, then gradually the universe. The depiction of Chito/Yuu as "gone" without "dying" could be an expression that they are part of the core underlying principal of the universe (the "will to life"), and thus maybe part of us even if they no longer exist in the story.
In January, about 5 days after the last chapter was posted, tkmiz tweeted "As for Chito and Yuuri, they're next to me eating pot-au-feu."https://twitter.com/tkmiz/status/953650250165583872
I think that's in support of the theory that Chito and Yuuri exist wherever we want them to.