I define "malware" to mean software that intentionally subverts the desires of the owner of the computer (unintentional subversion is a bug or a miscommunication).

Apple arbitrarily restricts you from using your applications (obsidian) to read and write your data in a way that you can sync, to no fault of its own, your own, or the syncing service.

I strongly encourage you to try associating this kind of behavior with an unfamiliar organization as a mental exercise. How would you feel about that? Someone else restricting your access to your computer such that you cannot use your applications how you want, through no technical fault of their own? I bet that would see that as a problem you would want to fix right away.