Thanks @gr5! It looks like the development build definitely addresses the behavior somewhat but not totally. However, going through my preferences more, I found changing "Z Seam Alignment" to "Shortest" (instead of "Sharpest Corner") or changing "Seam Corner Preference" to "None" (regardless of seam alignment) seems to totally fix it in both the dev build and in 4.6.1, at least a for a simple cylinder.