The sample part shown below demonstrates two through holes. One has a countersink on both sides, the other has a counter bore with a chamfer at the edge. The through hole that is considered a multi-step hole is the counter bore with the chamfered edge. This is because it is created in multiple steps.
When we choose Extract Machinable Features, you can see the multi-stepped hole was only found from one side, while the countersink hole was found from both. Multi-stepped holes are not fully recognized by AFR, the software knows that the features are there but it is fully combined into one “MS Hole”.
If you truly want full automation with AFR you need to break up the thru hole with a surface or something to make it realize there are two actual features to find. The drill can then be extended further on one side to break through.