See PHI574. Ref T13120. When you Ref Txx or Fixes Txxx, we mark it "unmentionable" to prevent the task from generating both a reference and a mention.
If you add a reference to an object (like a commit hash) to a custom remarkup field, there's currently no real way to prevent it from generating a mention, except that you can explicitly mark the PHID as unmentionable on the Editor.
This isn't exactly a first-class feature, but we technically do it in PhabricatorRepositoryCommitMessageParserWorker, and it probably doesn't hurt or interfere with anything to support it slightly better.
In Differential, respect any existing value and append new values to it rather than overwriting the value.