Yes, on linux at least (so most likely also on mac), the itch.io app uses a security wrapper to isolate executed programs (called firejail). It runs applications into a sandbox to avoid giving access to more data than necessary.
To run the VN, one has to remove the exclamation mark from the folder name, the 'EverythingChanges!.sh' and 'lib/py3-linux-x86_64/EverythingChanges!' files.
The bug was already reported to itch.io but their client didn't get any update since 2021.