Well, look at it this way: if he was still around when Viola collapsed, then that means that the pod only had to operate for two years on its own (facility two was shut down two years after the first facility went dark).
Considering that the gel fluid is highly oxygenated, and that being in them is close to a state of hibernation, I think it's not TOO much of a stretch (it's a stretch, but hey, it's supersoldiers XD) to just say that, because hibernation requires so much less oxygen, that it would last a lot longer than if someone was awake inside.
Maybe Cass wakes up when the oxygen levels are low?
Like I mentioned earlier, wakefulness would have to be induced externally. Kinda like if you were sitting in a car being flooded with carbon monoxide; you're more likely to lapse deeper into unconsciousness than actually become more alert.
Maybe it could just be a glitch in the pod waking him up years later (lol maybe some technician adjusted the controls of the pod wrongly), or simply the latches falling apart from rust or something, idekki