@Steen Schmidt I agree with you about leaving dependencies in their place by default -- we actually do that. It's simply that "C:\Program Files" (and the '(x86)' variant) wasn't on the list of locations where external components were expected. As always, things get a little tricky trying to support decades old paradigms.
Regarding a fix for this issue, can you try 2024.3.2761-rc2
here 👉 https://www.vipm.io/desktop/versions/
This should leave anything found under "C:\Program Files" or "C:\Program Files (x86)" along and not build it into the package.