Currently, this isn't possible.
The value of the flags read from the file are interpreted as if they were passed to Bazel through the command line: the path of the bazelrc does not affect where relative paths are interpreted from, and output base does not accept the %workspace% placeholder that we accept in bazelrc import paths. We could add to the syntax of output_base the option to make this possible, but would need to be careful and justify the change. For instance, any change to output_base's accepted path forms should probably also affect install_base and output_user_root, for consistency. Could you explain why you need this?