It must be noted that the Pre Crisis DCU clearly had various alternate future timelines. The Omac/Kamandi was one. The LSH was another. Barry-Flash's was another. Hal-GL's seemed to be another one.
DC once stated in a lettercol or editorial page that the various methods of time travel brought time travellers to different alternate futures.
The below link shows canon acknowledgement of the alternate futures stemming from the same mainstream DCU present era.
http://superman.nu/tales3/costumecostume/?page=17Said link clearly shows the Omac/Kamandi timeline being contrasted and in parallel with the Legion's future.
DC had many alternate timelines that were established as being alternate timelines; the Earth-1 Batman teamed up with Kamandi on one occasion in BRAVE AND THE BOLD, which clearly indicated the Kamandi future on display there was an alternate timeline.
Tying all this back into the opportunity Crisis had, and squandered:
Crisis was an opportunity, finally, to clarify and decide what was IN the DC Universe, and what was out; what was an alternate universe and what wasn't, in other words.
It was an opportunity to set once and for all as ironclad editorial policy that there are not going to be two or three mutually contradictory Atlantises, two or three mutually contradictory explanations for what it was that killed the Dinosaurs, two or three mutually contradictory explanations for the dominant life form and history of the planets Mars and Venus. In other words, to set everything in concrete, to put everything in stone, to make sure when the future or Atlantis is visited by Supergirl, it is the same future or Atlantis visited by the Flash or Aquaman. But if there was to be any destruction it would be achieved in the name of building something up that makes sense.
Here we can start to see where Crisis started to go wrong: the writer/artists (boy, there's an anxiety-inducing phrase there if there ever was one) like Keith Giffen, Mike Grell, and yes, my boyfriend little Johnny Byrne, mistook this act of negation, for the ENTIRETY of the role of building a new DC: negations were not used for the purpose of creating histories that made sense, but negations and invalidations of beloved stories were made just for sake of invalidation and negation. In other words, they didn't cross things out so we can have one cohesive explanation for the death of the dinosaurs; they crossed things out
just for the hell of it.