I don't buy the "came from the future" origin anymore, because there actually isn't really anything that implies that the Denliner crew are from a future. The dimension the trains and Kingliner roll around in is similar to the Persistence of Memory painting. The Stationmaster and the Owner are dopplegangers, and that was explained by Owner saying they only looked alike because that was how everyone saw it as.
I think it's more likely that all the stuff related to Den-O, Zeronos, Gaoh, Yuuki, etc. are manifestations of this "outside time" dimension. The Denliner crew (sans Hana, who was picked up from a timeline that was erased like lots of others whom we see in Kingliner) isn't from the future, they exist outside of time and safeguard its natural progress. They're physical manifestations of something more abstract.