By the way, famously neutral Switzerland is not in the EU, nor do I think it is ever likely to be, but it is definitely in Europe. So... guaranteed to evoke a violent reaction from police is to challenge their right to "define the situation." --- David Graeber citing Marc Cooper
For me, Europe is a geographical term more than anything else. The excerpt above that starts with "Geographically Europe is a part of..." best describes Europe as such.
This is true for me too - and when I read "center of Europe", I can only think of the geographical sense of "Europe". BTW, the Southeastern geographical border ambiguities shan't change the center much - the Caucasus Mountains - Kura river difference is only a 100 km wide strip, the Ural-Emba rivers idfference is roughly 500 km x 500 km, altogether a difference of 0.33 million km² - in a 10 million km² area.
You can visualise it on another relevant map from the Wiki article (here the Emba and Kura rivers are the borders; Georgia's and Azerbaijan's northern border is the Caucasus Mountains, the Ural river follows Russian-Kazakh border half-way East and then turns South):
II Europe, according to one commonly-reckoned definition II Extension over Asia of the continuous territory of a European state II Geographically in Asia, considered European for cultural and historical reasons *Lunatic*, n. One whose delusions are out of fashion.