I haven't noticed any problems yet.
I teflon moly coated some royal ordnance mags. Only wear on them was from the mag catch since I refinished them. (Don't think I cured the finish properly though. Direct hard abrasion from sharp objects will flake it off.) But the rest of the mags finish has little or any wear from insertion/ejection.
I suppose if you were really anal you could teflon coat the lower as well, or get a polymer lower.
Since the mag catch appears to be steel and have sharp edges (under tension when inserting/removing), I suppose the wear on the finish of the mags is normal.
According to the directions i can reapply and rebake to touch up spots after sanding them.