Glad I can help Eric!
More or less, it may not be the best (or a good at all) approach but it seems like a decent workaround.
You can read in the credentials in with Boto

session = boto3.Session(profile_name='some-profile')
dev_s3_client = session.client('s3')

from the shared config but yes you may need a separate script to update the values (which I don't think needs to necessarily use Boto) or maybe load the clearml.conf from a shared space (of course that adds other dependencies)
The Config vault vault definitely seems to address this (it's also an Enterprise feature). It looks like you can update config through the UI and merge into the config file while ClearML and ClearML Agent are used but I'm not sure whether that could still cause any blips. It comes with this "Productivity tip: Keep the vault disabled while you edit your configuration, and enable it when the configuration is ready."