Problem

You can only get the path of the "first folder" that you opened in the project and the full path to the file in question, but you can not use variables in substitutions (e.g. ${file/$folder//}). It's also restricted to one folder only (i.e. the first one), but that will rarely be a problem.

Example use case: You want to use python -m path.to.module in your project dir instead of executing the file directly.

Solution proposal

Provide $current_folder and $file_relative_to_folder variables. The variables are filled by iterating over all folders in the project and will be set from the first folder that contains the current file.
The resulting build system would then look as follows (hope I got the regex straight):

{
    "shell_cmd": "python -m ${file_relative_to_folder/([/\\\\])|((?:__init__)?\\.py)/(?1.:)(?2:)/g}",
    "working_dir": "$current_folder"
}

Workaround

Something like this:

{
    "target": "custom_python_module_build",
    "file_path": "$file"
}

import sublime_plugin


class CustomPythonModuleBuildCommand(sublime_plugin.WindowCommand):
    def run(self, file_path, **kwargs):
        for folder in self.window.folders():
            if file_path.startswith(folder):
                relative_path = file_path[len(folder):].strip("/\\")
                relative_path = relative_path.replace("/", ".").replace("\\", ".")
                kwargs['shell_cmd'] = "python -m %s" % relative_path
                kwargs['working_dir'] = folder
                self.window.run_command("exec", kwargs)
                return