It seems like in some places Moodle only sends plain text emails, which is a pain.
See:
https://tracker.moodle.org/browse/MDL-41300
https://tracker.moodle.org/browse/MDL-50071
https://tracker.moodle.org/browse/MDL-51157
https://tracker.moodle.org/browse/MDL-61617
https://tracker.moodle.org/browse/MDL-61649
(And vote for those issues)