One possible alternate conclusion could be that perhaps Serana's memories aren't quite as good as we're lead to believe. She certainly appears to have a good memory and seems sane enough, but given the fact that Elder Scrolls have a tendency to make anyone who reads them go blind and mad, it's no telling what kind of devilry it could have played on her whilst in her suspended state, regardless of reading it or not the sheer exposure over such a long time could have unforseen consequences. Again this is going back to the deus ex machina but we have no real way of knowing how the Elder Scroll could have impacted her "memories", I find this a more logical conclusion than attempting to bend every other possible truth around her apparent "surprise at a cyrodiilic empire"
However, her surprise isn't the only evidence we have for the length of time.
Durnehviir speaks of coming to the Soul Cairn during a time when dragons were vying with each other for territory. This would almost certainly be after the Dragon War, when the remaining dragons were left leaderless after Alduin's banishment, since I can't imagine Alduin allowing this kind of extensive infighting under his rule. However, since there were still plenty of dragons around, it had to be before the Akaviri showed up and began their extermination campaign under Reman.
His bargain with the Ideal Masters was to keep watch on Valerica, which means that she was already in the Soul Cairn when he arrived, and Serana had already been locked away. Thus, the time frame must be somewhere between the late Merethic Era and the end of the First Era even if we assume Serana's memory is flawed.
Another bit of evidence comes from Serana asking the identity of the High King. If she had been shut away before the reign of King Harald, I'm not sure this question would have occurred to her, since Skyrim was not truly an independent nation before Harald, who formed the first Moot and is considered the first true ruler of Skyrim.
Given her comment about a "war of succession," it may be that she was familiar with Borgas and the war that followed his death. This would imply that she was locked away during the interregnum between the First and Second Empires, which could explain her surprise at the existence of an empire in Cyrodiil even if she was familiar with the Alessian Empire. It would also be congruent with Durnehviir's story, as there were certainly still many dragons around at that time according to Paarthurnax and the story of Olaf One-Eye.