[CI] Allow configuration script to override CI defaults.

When we originally discussed `--ci-defaults` option, I thought that these defaults can be overridden by additional options. E.g. `--ci-defaults --option-X=val`, so that if `--ci-defaults` sets `--option-X`, users can replace the default value.
Unfortunately, I don't see this requirement to be documented in the code and it seems to be not true for options modified inside this `if-statement`.

_Originally posted by @bader in https://github.com/intel/llvm/pull/5091#discussion_r763010083_