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The executables aren't signed which is probably the main issue. They want executables to be signed with Extended Validation (EV) code signing certificates. It will get rid of the unknown publisher warning and over time I guess their AV will also start trusting you as a publisher.
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It sounds like an EV code signing certificate will outright get rid of the warnings. An OV code signing certificate is a lot cheaper and it won't be marked as from an unknown publisher but there will likely still be warnings. It would presumably get better over time though.