Safari Bookmarklets that invoke a custom scheme yield a warning like this in 10.12.2.
There’s a Cancel/Allow confirmation alert each time you invoke the bookmarklet, even multiple times for the same app in the same session. It’s really annoying. I often use to bookmarklets to create blog posts in MarsEdit and to archive Web pages in EagleFiler.
The (relatively recently) redesigned confirmation dialogs don’t help matters. I thought it was a scam on first sight.
Some people say that Safari’s newish iOS-style alerts are supposed to help users distinguish alerts that Web sites create via JavaScript from alerts created by apps or the system. That makes it harder for a site to trick you. That sounds nice in theory, but of course the distinction is absent on iOS. And, more importantly, why then is Safari presenting this bookmarklet alert as if it were from JavaScript?