After applying the cap holes modifier, I am trying to figure out quick solutions in re-topologizing the new face that gets added onto the poly. Below, you can see an example with cap hole modifier being added onto the editable poly. But, most often---when this modifier is applied, the new face being added is wavy smooth or messily triangulated. Is there a sort of smoother, reliable cap hole option or is the user doomed in having to insert loops, move around position of vertices, etc.?
You could try rapidtools, it's a collection of scripts. Free, but you have to register to download if I recall. One of them does a quad cap. It is still recommended to do different surfaces at a time though. So you'd bridge that small section of side faces first, then run quad cap on the bottom hole. It's something you have to play with to get used to. The orientation, or flow will be wrong many times, but if you use it in vertex sub selection mode you can control the direction better.
https://rapidmxs.com/store-main/rapidtools/
Edit: here's a video of it in action.
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