Duplicate Entry in ALTER TABLE (and in OPTIMIZE TABLE)

A few weeks ago and in MySQL 5.7, I had an ALTER TABLE that failed with a duplicate entry error.  This is old news as it is happening since MySQL 5.6, but I only saw this recently because I am normally using online schema change from the Percona Toolkit (pt-osc) or GitHub's online schema migration (gh-ost).  I do not like that and I am disappointed this has not been improved, so this post is partially a rant, but not only, because I explain why ALTER TABLE is failing and I give solutions to avoid the failure.