First of all, regardless of what the game is called and what you erroneously think, most of the timeline covered by Europa Universalis was certainly NOT the period of "Western dominance and preeminence". That would be the 19th-20th centuries, which is covered by Victoria II.
Secondly, the Spaniards were able to conquer the Inca and the Aztecs only due to a great deal of dumb luck, cooperation by ambitious natives, and the fact that Mexico and Peru already had fairly sophisticated, centralized polities where killing/capturing the emperor meant that the entire state fell into your hands. Elsewhere, such as in modern-day Chile, the Spaniards failed to subjugate the native Mapuche, Huilliche, Picunche, and other peoples even after 300 years of conflict and tens of thousands of Spanish casulaties (see:
https://en.wikipedia.org/wiki/Arauco_War).
Thirdly, having "Westernized" African and Asian states in the 17th-18th centuries is not so unreasonable as you seem to think, since several real-life states
did adopt Western technology (particularly military technology) wholesale and began manufacturing Western firearms in large numbers. The Kingdom of Mysore in South India, for example, manufactured tens of thousands of flintlock muskets indigenously, and was able to defeat the British in several battles in the 18th century (they were ultimately defeated in 1799 only after the British East India Company allied themselves with other major Indian powers, in particular the Marathas and the Nizam of Hyderabad). Even many Sub-Saharan African polities like Benin, Dahomey, Asante, and the Yoruba city-states were manufacturing their own firearms and gunpowder by the 18th century. Therefore, I don't see anything extremely "ahistorical" about a few Asian or African states "westernizing" and being able to field armies with similar technology and organization to Western states during the time period in question (if we were talking about Vicky II, I would have a different opinion). What is far more "ahistorical" is the ridiculous nerfing of great powers like Ming China in 1444 or the Mughals in the 1600s (whose total income should be greater than all of Western Europe combined).