Nearly every map made in this or last century
is a 3D model first. The first such model was made in 1745 by
César-François Cassini de Thury
From such a model, a (until now typically 2D)
map projection is chosen and the map drawn according to that, using whatever symbols the map-maker chose for features like height lines, waterways, roads, points of interest or labels.
This is the 21th century. Yes, people
do travel with 3D models around the Earth nowadays. Anyone who has a device with GPS and a map application which uses this GPS data has such a 3D map model with them. If they weren't, the devices couldn't tell if you're on or under a bridge. It's also usually just doing the same thing a cartographer does for display: Chose a map projection, display the map in this one as a 2D picture.
Yes, the pseudo-3D map of EU4 is very basic. I wish Paradox would finally make it a
real 3D map, not devolve into pre-18th century technology level ...