A little confusing, but the picture ties it together nicely. Unfortunately you'd still need a ground for the stock flasher in place so it's not exactly that simple, but that's the idea. I edited your pic to include the ground for the stock light that would bypass your splice connector. Your idea should work just fine though.
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That's a clean enough solution I may just switch over to that if I get some freetime; the wiring port going to the outside of the bike via undertail is getting a little crowded.