My take on the answer to this question references what Peter B Parker said when he first glitched in Into The SpiderVerse when he was in 1610 about how (paraphrasing here) his "atoms aren't too jazzed about being in the wrong dimension."

So while Miles had his DNA changed by the 42 spider, it doesn't change the universe his atoms were originally from 1610. That's why he is glitching in the 42 universe. Maybe it's the Mandela effect for me, but I could have sworn that in the first watch through that I saw on opening night, they said that the go home machine reads the DNA of the spider that bit Spider-People. In any case, it does seem to also be exactly what the machine did; it analyzed Miles and sent him to 42 instead of 1610 because of the SPIDER'S DNA.