My very uneducated guess is that it seals the wood, and used if they are using very open grain or porous wood. You certainly wouldn't need to do that on Maple. And the gray color could just be an undercoat or primer, that is designed to seal. Again, this is just a guess with my best Magnum PI mustache on. I'm probably wrong, but it's a good bluff.
yes, some of the companies use/used it as a sealer. Old Ludwigs had white interiors or clear, Rogers had grey as did Gretsch. Most used it to hide the bad grain patterns of the wood. These days a clear coat is used and, yes, it can affect the tone. Some swear for the better some for the worse.