Not sure about PhysicsImposter, but you might consider migrating to Havok physics (i.e. physics V2). With Havok, you can use PhysicsAggregate (a convenience function designed to help migrate from Physics Imposter), or generate PhysicsBody and PhysicsShape directly. Here are some tips, including scaling, on using PhysicsBody and PhysicsShape in Havok. Scaling a mesh in V2 (aka Havok) requires regenerating the PhysicShape.
Instead of automatically generating the cylinder then scaling, you might consider calculating the radius and height from mesh points. You could include only the desired submeshes and/or children meshes in the calculation. Be sure to use mesh points in world space.