Yes, and that irks me. But is boils down to the same thing as calling USAers "Americans" or even "North Americans". It's not necessarily wrong to do so. Words have a common meaning and a technical meaning. Europe is one of those words that has so many meanings that it is best avoid in any technical writing.

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...

A society committed to the notion that government is always bad will have bad government. And it doesn't have to be that way. — Paul Krugman

Beyond what Migeru responded, I'd like to emphasize this part of Denny's comment:

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.}