Well going by the modern era's interpretation of events, the wrinkle in this idea is that now we have to view all X-Men past events through the lens of Xavier already having the benefit of Moira's past-life knowledge by the time he ever formed the X-Men.
So as far as current events and definitions go, logistically, perceiving something like X-Men Forever through that lens means that the definition of omega that Xavier would be using there for Jean and Bobby would be the same as the general understanding of omegas from Moira's ninth life......where we know that omegas were an established classification on Krakoa given that its fall came about because of the generation of chimeras Sinister faultily engineered just from omega DNA.
So in essence, Xavier 'now' said that Jean and Bobby were omegas because he knew from before he ever met them - thanks to Moira - that they were omegas in that past life. And by extension his understanding of what that meant would be the same as what we're working off of now.
LOL, headaches, the true legacy of logistical retcons.