Maybe over complicating it? I've never had a problem cutting the thread when tying in the gills and pushing the bead over with the wide opening towards they, nor have I had an issue with crowding the eye (when using the appropriate sized bead for the hook). One trick I use and can be seen in the pic, is catching in the gill material through the middle close to the hook eye and doubling it over on the the first thread wrap then pulling both sides up and lashing down with a few more wraps.. This way it never makes contact with the smaller opening on the back of the bead and completely hides the bulk under the bead.
Have you tried my trick yet? Give it a try, you might find that it is not over thinking at all.