cmake-format should automatically use the config file in the directory: "You may specify a path to one or more configuration files with the --config-file command line option. Otherwise, cmake-format will search the ancestry of each infilepath looking for a configuration file to use. If no configuration file is found it will use sensible defaults."
When running it from command line, it works, but when running it from QtCreator it is ignored.
I tested with a cmake-format.py file near a CMakeLists.txt, with this config:

with section("markup"):
  enable_markup = False

This config disable the formatting of the comments.