I think you've missed the point of his question, as it's a bit off-topic for this thread... "Please forgive my ignorance but if you are digiscoping through a camera lens with autofocus capability..."
I'm interested in knowing the answer though - can an autofocus lens compensate completely for slight misfocus on the scope, or do both aspects of the setup need to be in perfect focus?
In short, yes, an AF camera can compensate for the scope being slightly in/out of perfect focus. When I digi-scoped with a compact camera, my typical focussing technique would involve half pressing the camera's shutter to see if it would lock on. If not, making a slight rotation of the scope's focusser and then trying again would usually do the trick. If the scope isn't close to being in focus to start with then the AF won't lock on.
In theory, if using a DSLR or compact system camera (with camera lens between the camera & scope's eyepiece/adapter), you should be able to use the same technique, but
only if the lens has an internal focussing mechanism. However, most of the lenses I've tried don't have internal focus-instead they extend during focussing, and some also rotate at the end. Therefore you risk straining the focus motor and also causing the camera to rotate! neither of which is advisable/desirable.
In such cases it's best to activate MF on the lens (thus eliminating the risk that the AF motor will kick-in) and focus only with the scope.
When Swarovski introduced the TLS APO adapter, they were basically simplifying the complex issue of which lens to use for digi-scoping? It's basically a fixed focus 30mm pancake lens built into an adapter, that is optimised to work with Swarovski Scopes. It can be used with a wide variety of camera systems (via a T-adapter specific to each different bayonet fitting). Therefore you only have the option of focussing with the scope when using the TLS APO.
It's not unusual to find that having focussed the scope by eye, and put the camera/adapter on the back, that the image on the camera's screen is slightly out of focus. The degree to which it's out of focus will vary from person to person depending on your eyesight, but a quick re-focus usually corrects this before taking the picture.