Please see GM's Bulletin regarding this type of "Surface Conditioning Disks".
https://static.nhtsa.gov/odi/tsbs/2016/MC-10082814-5448.pdf
Sure that comes up everytime just like the "oh my God don't weld around chlorinated" but that's speaking of internal engine bearing failure and was allegedly precipitated by cleaning heads with woven abrasives.
I'm far more lax on cooling system stuff. I'm sure the water pump doesn't appreciate it but in most cases cleaning a water pump mating surface is VERY different than a head or intake on the engine.
Obviously, use your own judgement but there have been several water pump surfaces I just couldn't get clean in EVERY spot to my satisfaction, so I do what I can with a scraper and then kiss the problem areas with a woven abrasive if needed. I'll generally try to block off ports with newspaper or tape, and a quick rinse with water theoretically helps to wash away some of that abrasive -- again wp surfaces are generally vertical while upper engine is horizontal and thus more problematic.
And yeah, I know most surfaces don't have to LOOK clean, they just need to FEEL clean to your fingertips, so no I'm not trying to polish every inch to bare, shiny metal.
TL;DR - be smart