I am specifically referring to the handling of Epics in the top-level progress indicator, which is not addressed in that work item.

You are certainly welcome to add that case just to make sure it gets covered. I expect the issue would be automatically addressed as they are both Plan Items and the crux of the problem seems to be counting the "container" for the children (so all child work items are estimated, yet 1 of N, the parent, is not, so you can't get to 100%).

Any work items that have no "weight" simply should not be counted at all in figuring out % estimated. No hours or story points? Then it should not be counted. Counting it as 100% wouldn't be right either as it would throw off the number. If you have 5 items with no estimate and 5 items with no weight, it should not say 50% estimated when in reality nothing is estimated. In that scenario 0% estimated would be correct.

This is more broken than I thought.
1. Because unweighted items are counted, as you mark weighted items complete, the estimated % goes down even though you haven't changed any estimates.
2. Story Points estimated % is broken in plans that use an extra level, such as "Marquee Feature". Both the story points completed at the top and the story points you see by hovering over the estimate do not show at all in these plans. Plans that only go to the epic level do show the numbers for story points.
3. Upon marking all items complete (closing out the sprint), the estimated % for stories and tasks become "--" instead of a number! This happens regardless of the actual estimated %, thus if you had marked items complete that were never estimated, that is now a secret you can only discover by manually looking at each work item estimate in the closed sprint.

Again, I like that story points are now included in % estimated, but they really broke things in adding this feature.

I have added this info to the enhancement you linked to, though clearly the problem is much bigger than what's listed in the summary of that request.