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 Jira
Created analogous issue for Confluence Data Center:
https://jira.atlassian.com/browse/CONFSERVER-99837

The basic secrets encryption was introduced in Jira:
https://confluence.atlassian.com/adminjiraserver103/secure-secrets-configuration-properties-1489808145.html
That would enable the plugin ecosystem to build on that too.