IMHO, as long as the "marring" is not structurally compromising the strength of the rivet head, don't worry about the "cosmetic" aspect. Your paint prep and final paint coats will easily cover any cosmetic blemishes. Do try to fit the rivet-puller nosepiece to closely match the rivet mandrel to minimize the potential for marring, but don't obsess about it.
David Heal - Windsor, CA (near Santa Rosa)
EAA #23982 - EAA Technical Counselor and Flight Advisor; CFI - A&I
RV-12 E-LSA #120496 (SV w/ AP and ADS-B) - N124DH flying since March 2014 - 560+ hours (as of Oct 2017)!
through June 2018.