Wow, forgot about this.
I've tried to replicate the issue, but can't.
I'm going to close this for now due to its age, but if you still feel it's an issue (or can narrow down exactly where the issue exists) I can take another look.
What I do note is that normal Stone Slab has no double slab variant in Extra OptiFine, so wouldn't be affected by CTM, and that the split top Smooth Stone Slab is from the customizer and not a variant. The variant for Smooth Stone double slabs are the tiles.
I'm pretty sure this is invalid