certctl: Always copy bundle fragments

When processing a bundle, we split it into individual certificates
stored in temporary files, then pass the name of each temporary file
to the creation function. Since the temporary files will later be
deleted, we need to force the creation function to copy rather than
symlink these files.

PR: 290957
Fixes: 986c43bd80e7 ("certctl: Add an option to copy files.")
Reviewed by: allanjude
Differential Revision: https://reviews.freebsd.org/D54081