Lol well I didn't care about that so much.
I don't want old IX plugins overwriting the new ones I explicitly install with ReaPack, every time I install a Reaper update. I imagine it might annoy others, too. That's why I said "I can't think of what might be the best possible method to resolve this", since making the stock IX directory the same as what's installed via ReaPack replaces the potential duplicate problem with a potential version problem.
I'll keep using my script, I guess, which I consider "step 2" of a Reaper install. It deletes the IX plugins (prior to starting Reaper) and also the stock preset file for ReaComp (since I find the stock presets just get in my way).