node-builder: Fix SHIM_USE_DEBUG_CONFIG behavior

[sprt]

Using a symlink would create a cycle after calling this script again when copying the final configuration at line 74 so we just use cp instead.

Also, I moved this block to the end of the file to properly override the final config file.

Merge Checklist

• Followed patch format from upstream recommendation: https://github.com/kata-containers/community/blob/main/CONTRIBUTING.md#patch-format
  • Included a single commit in a given PR - at least unless there are related commits and each makes sense as a change on its own.
• Aware about the PR to be merged using "create a merge commit" rather than "squash and merge" (or similar)
• The upstream/missing label (or upstream/not-needed) has been set on the PR.

Test Methodology

Local build