doc: extensions: doxyrunner: do not modify extension config

After the introduction of #41688, doxyrunner extension modifies the
fmt_vars content (from a variable defined in `conf.py`) when the output
directory variable is defined. This means that Sphinx will always get an
outdated environment and so will always perform a full build instead of
an incremental build. This patch makes a copy first to prevent this
situation.

Signed-off-by: Gerard Marull-Paretas <gerard.marull@nordicsemi.no>