Our SSO and user sync app could also use the ATL_SECURED properties, Bitbucket 9.0 introduced secrets.secured-properties property that enables defining custom properties for encryption:
https://confluence.atlassian.com/bitbucketserver090/secure-secrets-configuration-properties-1488590688.html

Could the same kind of custom property encryption be introduced to Confluence (and Jira too)
The basic secrets encryption was introduced in Confluence 9.1 https://jira.atlassian.com/browse/CONFSERVER-2146
That feature would expand on that.