So, when I go to consolidate & transcode a sequence why does PP insist on transcoding and copying every proxy file the project has created (in their entirety) regardless of wether it was used in the sequence? I would almost understand copying the proxies that are used in the sequence - although there should be a checkbox for that option. And I could (almost) forgive those proxies being copied completely rather than just handles (maybe the code to consolidate proxies and still keep them synced is too hard to manage) But everything? EVERY SINGLE PROXY FILE? That clearly is a major bug. And it's not just related to this project. It has been happening since I started working with Premiere on multiple projects all year.
It appears you're right - unreferenced clips have their proxies copied/transcoded. It doesn't particularly surprise me, the project manager is buggy and has lots of quirks. You could temporarily detach your proxies before opening the project manager: of course only really viable if you don't want to copy any proxies (otherwise you would have to detach only clips you don't want, which may not be obvious). Not ideal but it seems to work.
Sadly there are more problems with this "function" than this. A lot more problems. Speed being the biggest one. Another would be its lack of ability to create a trimmed version of a clip and instead just basically announcing "Can't!" and copying the entire original clip - even a 60min interview in its entirety for a few short clips.
Words cannot desribe how frustrated I am with PP's lack of ability to consolidate a timeline. I can only assume that the issue has not got a lot of attention because most PP users just do everything themselves on the same system.