We're starting to use a new application for meetings, and every time we click on a link to join the meeting in Outlook for macOS it launches Safari, then we get a prompt "Do you want to allow this page to open <Application>?"
Is there any way as an enterprise to auto approve that so the application just opens? I know it's a security feature, but there are certain applications we'd want to always allow.
There isn't any way to bypass the Safari protocol handler warning, which applies even to Apple built apps such as Terminal and Mail. However, I would double check to see why the links are hitting Safari in the first place. Has the client application been run before? Does its Info.plist define the protocol handler the link uses? Is the handler registered in the OS? You could use the ancient, but as of 10.13 still functional, RCDefaultApp for this, or the harder to use but more modern duti.
Vuze was the default until I installed Transmission. In Safari it now was "Do you want to allow this page to open Transmission?". I just had to start Vuze which came up with a "Do you want Vuze to be the startup item" dialog. Select yes and now it's back to "Do you want to allow this page to open Vuze?" when selecting a Magnet in Safari.