Happens without the mod, too. I'll be happy to re-add it. I only used the profile with a mod here to make sure I wasn't losing my mind entirely.
Yep, about at the 2 hour mark this guy appeared in the upper deck (slightly different village design from the other one but still surrounded by only half-slabs and glass).
I found this behavior in cases where I was trying to prevent a golem spawn in a certain area, and attempted to solve this by topping that area with half-slabs and glass blocks but ran straight into this defect.
I've found a workaround for this that seems to work in 1.8.x. Put a solid block underneath the half-slab, at a level at which golems would not be too short in any covered area underneath. Of course now my problem is that the golems are spawning on top of the half-slab (see MC-77620).
Added an image of a golem spawned on half-slabs without the use of any mods seconds before he dove off the edge.