You seem to be making a pickle! I would suggest you try and keep your filing system organised; the result is not less demand on the CPU etc. but rather less potential headaches due to not having to stumble around in a mess. I would not, and don't, let installers do their own thing since letting them do their own thing is a surefire way of adding disorganisation to your filing system. Some installers are better than others of course, but you don't know this until after you've clicked instal and then it's too late (e.g. look at your root folder).
For example, i have 2 main folders for plugins (Program Files\vst plugins and Program Files\Common Files\VST3) and inside those folders i have developer folders for their respective plugins. I got rid of all 32 bit plugins, but previously i had the same folders in the x86 folder also. This aids in organisation as things are in the same places.
I would delete all that extraneous stuff from your root folder. If the plugins don't work i'd delete them and reinstal with organisation in mind. If they're adamant about installing crap to your root folder i'd delete the plugin and write a complaint email to the developer.
ien's post in Program files vs Program files 86 was marked as the answer