I'm so glad I'm out if the apple ecosystem. It's nice I guess, but there's just so many weird unforgivable choices they make. Like the inability to turn off opening links in an application. I was so thankful that Firefox Focus didn't respect them. It got to a point where I just deleted apps that suddenly got opened because I clicked on a link in Safari or whatever. I think I remember it happening in private mode too. And on other applications. Does Apple think all of our accounts are tied to our real name or something? I thought they were good at this privacy stuff.
On Android it asks me nearly all the time. Not sure about the mechanism but its much better either way.
It's just a phone number on the website. It's macOS/iOS that decides that clicking a phone number should open FaceTime, and the restaurant has nothing to do with this - they just put their phone number on their website.