Etiquette for dealing with supervisor comments on written work
It is an important acquired skill to know when to gently push back against your supervisor or referees in your field of study.

You should not implement suggestions you are not comfortable with without asking for clarifications.  You need to know when to hold ground and defend your position in a courteous but firm way, and this might as well be in discussions with an open-minded and competent thesis director: you may have to yield in the end but in many cases gentle arguments are synonymous to constructive discussions.