Yes, the two formats are different. (But in my experience the package manager’s is actually much easier to work with.)
Yes. This is how both Xcode and the package manager handle packages.
They have no such customizability that I know of.
I solve this during post‐processing. My methods for loading coverage data into Swift, excluding dependencies, are here:
You can depend on the package directly, or use the source code as a reference while you write your own.