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Likely due to layout changes on YouTube's side, I had to change the CSS so that the overlay does is not partially on the seek bar. Specifically, I had to change to the following:
.ytp-arc-list { bottom: 5em }This seems to match the other YouTube button menu overlays. Though they don't seem to use the bottom property at all. If you ever refactor, it might make sense to keep the existing classes and styling, and only add additional content to the styling.
For me, though, the above is sufficient.