This has not been an issue for me… Perhaps you forgot to change directories in a step? Post 14 in this thread I outline the steps for constructing the SITL using Ubuntu 20.04 and python3.
https://community.dojofordrones.com/t/launchsitl-cant-find-main-in-module-in-error/638/14
Remember to remove the dronekit ‘exceptions’ library as it doesn’t work with python3.