I have a Conquest 3x-9x-40mm and I love it. I think it's just as good as the Elite 4200, except it doesn't have rainguard, but does have etched reticles.
I like 50mm objectives over 40mm ones. Why? Well, I like extra brightness and, something that is usually overlooked, there is greater eye alignment (not eye relief, but alignment).
I really don't care if a scope is mounted just a tad higher than a 40mm objective scope.
I didn't know that the 3x-9x conquest has a 50mm objective - it must be new? Still, for only $20 extra, I'd definately go with the 50mm!!
Zachary