It depends which towel and how you use it - more than just considering if it's a waffle weave or not. I use waffle weave towels exclusively to apply QDs/spray waxes and to dry. I use high quality towels - and have never noticed any marring.
Microfibers themselves are very thin. Much thinner than a human hair. I do not believe it's the style of the weave that can cause them to mar, I believe it's more the user's environment, how the towel is stored/washed, towel quality/composition, and technique of use.
Of course, one could argue towels with satin borders can mar - and a lot of WW towels have satin borders. However, I just haven't found this to pan out in real life. When you are using these towels to spread/pick up liquid - you aren't/shouldn't be using much pressure, so this may help things along.