F13 is one of those "use at your own risk" products. When paint oxidizes, it basically is degrading a very thin layer of the paint. F13 and similar products strip off that thin, damaged paint layer. So it's normal to see the paint color in your bucket.
If gutters have aftermarket paint, they may or may not hold up to the chems. If it's factory paint, it "should" be ok. But always spot test if a situation makes you nervous