You're right that the collector and emitter are not identical in size nor geometry nor surface area bordering the base. There's a nice cross-section about three-quarters of the way down this page[1] that shows the basic layout for a BJT. As to why we fabricate them as nested wells instead of side-by-side rectangles, I believe it is to maximize junction area relative to die area. These layers are exceedingly thin, so almost all of the junction is top-to-bottom, not side-to-side.

1. http://www.circuitstoday.com/monolithic-ic#monolithic-fabric...