Shouldn't be a problem. I've notarized plenty of fat binaries.
It supports back to Mavericks (10.9), so I would like to have two versions of a tool, a 32-bit version that works on the older systems, and a 64-bit one that works on more recent systems.
While this should work, I’ve no idea why you’d want to do it. The last macOS release that supported 32-bit machines was 10.6.8. If your deployment target is 10.9, there’s no good reason  to be shipping 32-bit binaries.
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Quinn “The Eskimo!”
Apple Developer Relations, Developer Technical Support, Core OS/Hardware
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 Well, there are some good reasons, but they’re quite obscure. If you think you need to do this, please write back with an explanation of your rationale and we’ll take things from there.