also, I like the machine stitching
I saw a BNIB pair up for auction on Ebay about two years ago. Another "shoulda-pair" I regret not acting upon. The flat welt is a nice little detail that makes the barrie-lasted boot look a little sleeker.
Nearly all color8 shoes/boots have this kind of dye stain. And the stain should only be visible under certain lighting.
Just wear them in good health.
If you can only identify the dyed splotches with bright lighting and close examination, I would keep them. I have a pair of color 8 SWB that are my favorite pair of color 8 shoes. Six months after purchasing them I noticed the slight splotches (very similar to yours) when cleaning and brushing. I am still perfectly happy.
You and others may disagree, but that is certainly your call and you would not be wrong to return.
Those are your only two options given a defective pair of $800 boots? Store credit or keep them?!
I would personally raise hell over something like this.