Keep in mind that some of the organic materials used in potting media can release pigmented chemicals. Bark for example, can realease tannins, which are brown and water soluble. If the velamen absorbs the tinted liquid, it will appear brown.
I think it's also important to understand that an orchid root is not two-layered - velamen and central core - but is actually typically 6-layered.
Starting at the interior, we have the stele, which is the wiry core remaining in a dead root. Outside of that are the thin endodermis, cortex, exodermis and then velamen, which is simply dead exodermal cells that act as a sponge to store water.. The 6th "layer" is the root cap, which protects the root meristem at the tip.
This microscopic cross-section of an orchid aerial root shows the 5 distinct layers quite clearly. You'll note the velamen only accounts for about the outermost 20%:
Ray Barkalow, Orchid Iconoclast
Using science and logic to advance orchid growing
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