I have now configured 5 x WR21 units by editing the config.da0 files and everyone has refused to move the PORT ISOLATE mode functionality from one router to the other.
After uploading the edited config, every router but be logged into an manually changed to port isolate mode.
The behavior you describe is expected, the port isolated / hub mode is not a config setting so is not automatically imported.
If you want to avoid to do it manually, a way is to edit the config.da0 file with a text editor, adding the Port Isolated command “ethvlan” at the end. Then, you would need to reboot the device twice. After the second reboot, the command will be applied and the router will be in port isolated mode.