What is the validity of doing 2D airfoil simulation for axisymmetric bodies?
Xfoil analyzes airfoils, not wings, and as such does not account for wingtip effects so its results are invalid for bodies of revolution or even low aspect ratio wings.

More generally, you can reference this answer about the derivation of wing lift from airfoil data. It boils down to the fact that aspect ratio has a massive impact on the 3D flow around the wing. For high AR wings the flow at most sections is close to what can be predicted with a 2D method, but this condition does not hold for slender bodies or near wingtips.

To phrase it differently, we can only apply the results from 2D simulations to wings by avoiding 3D effects. In the case of slender bodies, the entire flowfield is impacted by 3D effects. 

Since flow separation is dependent on the pressure field around the body, you need to have an accurate idea of the 3D flow to reliably predict separation points.