There's also a prophecy that Link is supposed to become the Hero of Time. Yet, he never becomes the HoT in the CT, because he changed history. Changing history/destiny is an underlying theme of the CT, between the HoT never being recognized as a hero, to Ganondorf dying forgotten instead of becoming the scourge of Hyrule, etc.
''Evil ruling all'' may not be a condition for sages to awaken in general, but it is presented as being the condition required for the OoT sages to awaken. And as said above, ''Evil does not rule all'' in the CT. The prophecy doesn't present any other alternaive scenario in which those specific sages are awakened.
Remember; evil ruling all, the coming of the Hero of Time, and the awakening of the sages are all a part of the same prophecy. And yet, neither of the two former parts come to pass on the CT. Why assume that the latter does?
Since the Ancient Sages exist in SS and they have the same medallions as the OoT and TP sages, isn't it a safer assumption to assume its them?
Also, both the AT(the stained glass windows in Hyrule Castle in TWW) and the DT(the sage town names in Zelda 2) both make it clear that the sages are known and remembered, but yet, even in TPHD, there's only a statue of Rauru, who was also one of the Ancient Sages; the identities of the other sages are not made clear. Why is that?
Not to mention, Master Works/Creating a Champion says that Ruto awakening and helping the hero seal Ganon away after he transformed through his power is what happened in the world of BotW; this only happens in the AT ending of OoT(where he's in his beast/pig form for the final boss fight) and the DT ending(where he transforms into said form before being sealed by the princess and sages, like what that passage from MW says). Even if you're hellbent on the OoT sages awakening in the CT, the history of the CT does not match the history of BotW.