You're completely right, all SET, MSG, LOG, and ZIP files found in Airio root folder on start, reload, and some other actions are simply copied to appropriate subfolders, overwriting the existing files. That's usually the required and expected behavior, say in case of updating MSG files from new language pack. But you're also right sometimes this may lead to certain issues, such as with the default SET file.
Now there's the question about what can be done. The easiest solution is not to copy default SET file from the updated Airio archive. Take just EXE and PBD, and also check what's new in standard config files, that is CFG, TCD, and SRV.
Another option would be to automatically create a backup copy of files already existing in subfolders in case new files with the same name are found in root. But they really need to be copied and must take precedence over the existing files, or some other features (such as remote updating using !dld command) will cease to function.