I am using the Connectome Mapper v3.0.0-RC4. I tried to import the BIDSLayout with the line you suggested and it worked.
As you suspected, the main problem was given by the GUI. Although I used the environment file you provided, tt did not manage to update the version of some of the derivatives that were already installed (for example, the installed version of pydicom was 2.1.2, while the required one is 2.0.0). After re-installing these packages one-by-one, the GUI works!
Thanks for the help!