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When Neogit is shown as a floating window, the background by default falls back to Normal, whereas the floating border falls back to FloatBorder. FloatBorder may have a different background colour to Normal, which can result in a slightly messy overall effect.
I would suggest:
Adding a NeogitFloatBorder highlight group which by default has the same background colour as NeogitNormal
Possibly also adding NeogitFloat, which would take priority over NeogitNormal in the event that a floating window is used.
I might be able to find some time for a PR if you like the sound of this :)