I could possibly see that the Odyssey would become the next version of the Base or at least a mobile HQ for Aloy and Co, given that Sylens said that the full extent of the Apollo database was still onboard and locked with a variety of security measures, maybe Aloy and Beta both using Alpha Clearance as it was originally a ZD subordinate function could override it and needing to be physically present,
I could also see the Odyssey or at least it smaller shuttle being used to transport Aloy and Co across the planet in relativity fast timelines if locations such as the Quen homeland and areas from North America were to appear in the next game, in addition to being the vehicle that would allow Aloy and Co to attack NEMESIS in its physical form while it was in space
I could also potentially see that Sylens could have been less than truthful about the number of remaining Zeniths, maybe there could have been a Zenith on board, either one who was willingly working with them or one of the “good ones” as Tilda called them who would have been imprisoned for maybe going against the other Zeniths at some point during their return trip, at the time of the attack on the Zenith base and he would have captured and sought to interrogate the Zenith to gather information about NEMESIS and learned about Walter during the event