Modal prompts where applications (and websites!) request permissions are an absolutely terrible UX. Sure, they're very easy to use and convenient, but they're easy to use to accidentally grant very wide access to untrustworthy third parties.
Granting permission to pages should be, as you say, an explicit user-initiated flow via a permissions panel. The same should be so for sandboxed desktop applications. Does an application want to continuously record your screen? Then it should be granted this permission explicitly via a permissions control panel. It shouldn't be able to show a modal dialogue where people just click "yes". Many times, with good reason: they simply don't understand the technicalities of what they're being asked.
Granting permission to pages should be, as you say, an explicit user-initiated flow via a permissions panel. The same should be so for sandboxed desktop applications. Does an application want to continuously record your screen? Then it should be granted this permission explicitly via a permissions control panel. It shouldn't be able to show a modal dialogue where people just click "yes". Many times, with good reason: they simply don't understand the technicalities of what they're being asked.