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Surely you can turn on option 3 indefinitely for local builds at least. Otherwise Apple kills the ability to develop any software while offline or behind a firewall.

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Gatekeeper only applies to software downloaded from the internet. Browsers set the "quarantine" attribute for downloaded files, and then Gatekeeper kicks in on first launch.

Software that you build locally, or that you install with a package manager, is not affected.

The goal of Gatekeeper is to keep your Mac safe -- not to control what you can do on your Mac.

Would something like "cat a.out > b.out" bypass Gatekeeper? I am always puzzled by apps which know the origins of files that they open.

Yes that would bypass it. It's metadata set in the filesystem not a part of the file itself.

What I usually do is:

    xattr -d com.apple.quarantine FILE

It removes the extended attribute from the given file.

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