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It would be fine except the user has no way of proving to the developer they already bought the app, which would be handy for continuing to get updates elsewhere. Apple doesn't share anything about who bought what.

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This isn’t quite correct. Vendors can and do verify Mac App Store purchases with applications deployed outside the Mac App Store. The installed bundle contains a receipt you can validate yourself. I think there is a gap where if you delete the application, then Apple removes it from the Mac App Store, you can’t reinstall it to get the receipt, but that’s a bit of an edge case; the majority of customers will be “upgrading” from the Mac App Store version to a newer non-Mac App Store version in a situation like this.

Also, if you have user accounts and plan for it in advance, you should upload the receipt to your server and associate it with a user account, which makes some things like this a lot easier.

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