Only when an app is distributed from their store though? You can request a developer certificate, notarise your apps and deploy them from your website using any API you desire...
That's incorrect, some MacOS APIs (I'm not sure why you think a website is involved here?) require special entitlements (regardless of how they're distributed) and you cannot use them with a normal developer certificate - you need to pay the Apple tax and speak with someone at Apple directly to get them.
