Is all the port of embarkation aware of this 144 hours transit free visa

This could be a problem, indeed, because not all the employees at the airport around the world are aware of this option. However, the passenger using this option has to point the employee, in case of his/her ignorance, to Timatic where all these details are written in detail. Also, one should insist for a more informed or more knowledgeable person as his/her supervisor probably is.

By the way PK, you should be aware that Malaysian citizens are not eligible for 144 hour visa free transit, but just to 24 hour visa free transit, so maybe this is the reason why they were refused to be issued a boarding pass.