Any application that you choose to download and run with your Linux user account has access to all the files (data) of all other apps, the only isolation is at

Any application that you choose to download and run with your Linux user account has access to all the files (data) of all other apps, the only isolation is at the user level (the rwx that you mention), not at the app level. It's not reasonable to expect non-technical people to create a user account for each app they want to download and use from the Internet.