No perl, please it is too big. But seriously, it is up to the extension maker.
Choices are:
1. Display files that the user should add to .filetool.lst to persist settings.
2. Make symlinks to home directory, that way backup is automatic.
3. Create a utility to repack extension with user settings, e.g., getFlash10.
As extensions are freely contributed by the community, we can only suggest that these options be deployed.
Check .info file for option 1, otherwise post a message in TCE area so that each contributor may respond.