Regarding Estonia, there's a rather good chance that accuracy isn't the only thing looked at when determining starting de jures.
With Estonia in the Wendish Empire, that empire is much closer in size to the surrounding empires (excluding Carpathia, which of course is rather small), while Scandinavia would be much larger than its neighbours if it got Estonia (with Estonia in the Wendish Empire it loses to the HRE and is only slightly bigger than Russia and Britannia), so having Estonia in Scandinavia might have balance implications in the region.
The AI also (seems to) try to expand inside its primary de jure structure first, so if Estonia was inside Scandinavia the Norse would assault Estonia quite early and Estonia would (try to; they don't really have a good CB, particularly if Scandinavia starts to become non-pagan) expand inside Scandinavia, and rulers in the Wendish Empire would be reluctant to attack Estonia with it in another de jure, which might lead to strange behaviour.
Having Estonia in Scandinavia would also create issues when coupled with the possibility of the new exclave rules, which on the harshest setting would make Estonia independent of Scandinavia unless you create an overland connection (which isn't guaranteed to be feasible, since there's no guarantee that you'll have a CB for it) and thus could get the AI stuck in a loop of "Conquer Estonia" -> "Lose Estonia upon succession" -> "Conquer Estonia", which seems potentially problematic (and "Who cares about the AI?" is not a sentiment I think is good for the game).
The Wendish Empire also looks fairly nice when it reaches the Gulf of Finland, while a disconnected part of Scandinavia in that area would look rather weird, though aesthetics probably is rather far down the list when it comes to priorities. However, securing most of the southern coast of the Gulf of Finland would also seem like a sensible move for a Wendish Empire and something that could be part of their initial terretorial claims, and an Estonia that's getting powerful could would possibly find expanding to its south to be rather appealing due to the proximity and having decent CBs, and, while that's not moving into an area held by the same culture group, there are other empires where different culture groups fight it out, e.g. Britannia (Norman/Anglo-Saxon/English vs. Celtic) and Hispania (Bedouin/Andalusian vs. Iberian + Central Germanic).
Also, there are Finnic/Suomenusko kingdoms in Volga-Ural (and Russia, which wasn't an empire in the era), which also is a fictional empire (and Scandinavia is only accurate in the first place if you count the Kalmar Union, which didn't come around until over half a century after the last start date), Tengri rulers scattered throughout a bunch of fictional empires, Slavic (both culturally and when it comes to religion) rulers in a lot of different empires (with the ERE being the only one existing in the era and not really being in control of the land where those Slavic rulers actually live), and so on, so it isn't like the devs have singled out Estonia for "incorrect" placement.