meson: Allow directory options outside of prefix

This bring us in line with Autotools and CMake and it is useful
for platforms like Nix, which install projects
into multiple independent prefixes.

As a consequence, `get_option` might return absolute paths for some
directory options, if a directory outside of prefix is passed.

This is technically a backwards incompatible change but its effect
should be minimal, thanks to widespread use of `join_paths`/`/` operator
and pkg-config generator module. It should only cause an issue when
a path were constructed by concatenating the value of directory path option.

Also remove a comment about commonpath since we do not use that since
<https://github.com/mesonbuild/meson/commit/00f5dadd5b7d71c30bd7393d165a87f554eb92e5>.

Fixes: https://github.com/mesonbuild/meson/issues/2561

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