You could also try to Target Weld tool. It's a MEL script.

From the author's site:
targetWeld
emulates the behaviour of the 3dsMax tool - snap selected vertex to location of a second vert, and weld/merge them.

https://www.users.on.net/neilandbron/

About your question,
Maybe you can better use Edit Polygons>Merge Multiple Edges IMO.

Yes, the poly's must be combined in order Merge Edge Tool to work. It works like this: select the Tool, then select the first edge, then the second, click again on the edges or enter and the edges are merged.