Update 1.3.2 brings in vertices auto-merge in edit mode:
When you snap vertices onto vertices of the same object you can now have those vertices be automatically merged together, similarly to how it works with default snapping in Blender.
Note that to do that you need to have vertices Auto-Merge enabled, it is a small icon on the top right of the viewport:
And if you don't want that functionality altogether, you can also disable it in the addon preferences.