Shouldn't we run it inside the current directory then? What does Cargo do?

Cargo doesn't fetch metadata for sysroot, only we do.
Once we tried to fetch sysroot metadata within the cwd but it resulted in applying some not-wanted configs to sysroot metadata like in #20250
I'm not sure which one is grater, the number of configs should applied to sysroot likewise in the project cwd, or the number of configs that shouldn't applied to the sysroot. But for something like the above issue, there aren't much thing the user can do to avoid the issue, so I chose not running cargo metadata for sysroot in cwd.