I know this thread is kinda old, but since I've been googling around for a while, I thought I might as well share that I ended up using the method outlined in the blog post here:
https://www.f-ax.de/dev/2022/11/09/how-to-use-vcpkg-with-universal-binaries-on-macos/
At least this explains how to get universal binaries out of vcpkg and there is a sample project for a universal cmake app...
Maybe this is also helpful for other people searching for this issue...