In practice, this is almost entirely going to be used for internal links within a domain - you are not going to want to prerender domains you don't control, because you can't be sure they'll be prerender-safe. And I suspect most internal navigation will be obvious to the user - it's typically clear when I'm clicking links in a nav menu, or different product pages on a shopping site. So I suspect your first issue will not come up in practice - users will typically not need to check the sorts of links that will be prerendered.

Tracking is a legitimate concern, but quite frankly that's already happening, and at a much finer, more granular level than anything this feature can provide. Theoretically, this gives the possibility to add slightly more tracking for users that disable JS, but given the small proportion of such users, and the technical hoops you'd need to jump through to get useful tracking out of this, it's almost certainly not worth it.