my doc (Check) simply took his prescription pad and scribbled "SCSA" in big letters and gave it to me, took 2 whole seconds, I took care of the rest. The lab in SD sent the container to our house, DH put his sample in, I dropped it off at FedEx. Done. I did not even try to get insurance to pay for it.
Your RE was probably planning on making your DH come to the clinic, and the extra fees were for the clinic to take his sample, package it and send it off. Much easier (and cheaper) to do yourself at home.
My other peeve with some docs - if the SCSA test comes back poor they say "it's OK we'll just do ICSI!" --- ICSI does not cure fragmentation. I actually had one idiot doc say we didn't need to do the SCSA test because we were doing IVF with ICSI already and had that covered. Wrong.