Thank you everyone for your comments.
Based on the feedback and our own discussions, we are going with this for now:
Instead of adding the root certificates, we have decided to ship a cert_override.txt [0] populated with the services we care about (OFTC, jabber.ccc.de). This will allow users to connect these services without the scary certificate warnings, and without us adding the root certificates to Tor Messenger. (When you add a certificate exception, it gets saved to the cert_override.txt in the profile directory.)
[0] - https://developer.mozilla.org/en-US/docs/Cert_override.txt