Should I be worried about these black marks?

Yes, she's fairly spritely, doesn't seem to be bothered about it at all. I've let her out in the yard for a bit to get some exercise and she's currently destroying my garden.
I really wish I knew what to tell you. You're right that it's not pecking injury, but I'll be darned if that isn't what it looks like. I wonder if fowl pox would make the "bruising" marks you see on the wattles.
 
Where is she being housed? Do other birds have access to her like being able to peck at her through a crate/kennel?

Pattern on wattles and the dark streak on her comb look pretty much the same to me in your photos. Back of comb there is some scabbing - could be from rub or peck. Ridge of beak also has new injury, possible from rubbing or sticking beak through wire or cage.

If you feel it's disease that you are dealing with and are hesitant to add her to your flock, then culling may be the most practical avenue to explore. If she's been roaming your property and you haven't been practicing biosecurity while tending to her and your flock, then IF it's disease, the others have been somewhat exposed.
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This may be a long shot and not applicable to you, but I wanted to put this out there and share my experience. Do you use wood ash or anything caustic in their dust bath, nest boxes, or coop? One of my hens had similar spots, and it turned out to be burns from the wood ash. We live in the southeast Georgia near the coast (US) and have very humid, damp weather. Wet ash is caustic. I’ll check to see if I still have a picture.
 
Hi carlaashdown. Not at my place, but I've only had the bird for a couple weeks and they were almost certainly present before I bought her. As I mention initially, the breeder was keeping his birds in pretty squalid conditions and I have no idea what sort of issues might have arisen from this.

Staceyh, interesting suggestion. I checked the photos on google for this and they don't look the same. It looks like favus is accompanied with white crusty stuff which this hen doesn't have.
I thought I saw white on comb in your pictures. Could be these old eyes.
 
Update - I've put this bird back with the other chooks. The black marks haven't changed but there is no more scabbing. The bird is quite energetic, but very flighty still. I won't let me near it. I've had leghorns in the past, but they've been been this scared of people. Anyway, given the marks have not changed, I'm concluding that they're scars of some kind. The bird may have been badly picked on before I picked it up, leaving permanent bruising.
 

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