I long ago gave up the fight and no longer try to coerce installers into doing my bidding. It's the path of least resistance and the path to the least number of hassles.
At one point my attempts at organizing plugins resulted in Kontakt DLLs in three separate locations on one computer, two locations for my Meldaproduction plugins and two locations for my iZotope stuff. I didn't know which versions were in what projects. That was my motivation for writing my little VST Inventory tool - just so I could figure out which DLLs were the "real" ones, which were old versions and - worse - new versions never implemented.
So aside from sample libraries, where location is important, I just don't sweat it anymore. I let installers have their way with me and enjoy a less-complicated existence as a result.