Your use-case looks like an argument for moving the external headers into some separate repository. Not that I personally care much about bundling or not bundling. To me the more important question seems to be whether to auto-enable the encoders/decoders that depend on the external headers and libraries or not.
At least nvenc will stay as auto-enable even with out-of-tree headers, except that it will obviously check if it has the required headers available.
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