You are quite right.
However there are protiend skimmers and there are... Protien skimmers.
I personally prefer to underskim arather than overskim for the very reason you mentioned. I have a prizm skimmer that gets aweful reviews for that very reason. I know others that use much more effieicnet skimmers and find that simple regular water changes keep things in check.
I opted for lower skimming because i use Natural Sea Water (until about a month ago i didnt skim at all) and i felt that skimming would take out the very essence that makes natural sea water so much more appealing to me than artificial salt.
I am currently testing the tank with my prizm again so see how much it extracts and i am amazed ! In the first week of operation i had the cup filled 3 times! So much for mineral mud saying that a skimmer is not needed....
Actually.. scratch that.. Their statement might be true, you possibly DONT need a skimmer on mineral mud but without a skimmer there sure is a load of crap left in there