If user macros are defined in a velocity template, they can potentially be included without rendering due to a Velocity bug https://issues.apache.org/jira/browse/VELOCITY-776

Ideally JIRA will update its internal version of Velocity1.7/VelocityTools>= 2.0 which contains the fix, released 17 JUL 2016. Currently JIRA 7.3 is shipping with V1.6.4

The workaround is put UserMacro definitions inside ./atlassian-jira/WEB-INF/classes/templates/email/macros.vm so they are defined statically.

Standard atlassian email notifications won't be affected by this as its templates are loaded statically

Update: Velocity 2.0.x is not yet released despite release date being set - the 2.0. release is actually available, so must be transitioning/being announced : https://dist.apache.org/repos/dist/dev/velocity/velocity-engine/2.0/release-notes.html