Didn't investigate enough so a bit of a facepalm going over the title, this is the expected behavior seeing that there are no edge groups in Blender so it's actually operating on the vertices. Should use weights instead but not quite apparent at first.

The tooltip for Emulate 3 Button Mouse explicitly says "doesn't work with Left Mouse Select option", so while Blender allows you to select it while its grayed, it still wont work.