NTX pipes are different than the SS pipes on my 1200 Sport. On the 12S, I did indeed remove some spots with 0000 steel wool (plastic bag flew up and melted onto one of the headers). I definitely would not take steel wool to my Stelvio pipes - there's a textured, gold-ish coating on them that will likely be worn off by steel wool.
Maybe check with the dealer about warranty? They may have seen it before or tried to address it with MG. No discoloration on my pipes yet, but only 2k miles so far.
Ok, great I was sure thinking they look anodized or something..
Honestly if getting them replaced (if successful) on warranty doesn't solve the problem long term (ie it does it again):
I'd much rather just get them fixed permanently with another process if one is available at my cost.
Done once and be done with it is my thoughts..
Mine definitely look like they could use some "love."
All just up in the area of where they exit the head and just at the area where it is making the turn downwards.