The first click makes a background app a foreground app.
This was designed that way to prevent accidental clicks when switching windows. Scroll your mouse over a link, the arrow will change to a finger pointer. Now if you do that for another windows, any app. That will not change because its not in the foreground.
This doesn't mean background apps are completely inaccessible. The messages app for example, you switch between contacts first click. However you cannot click a link from a contact first click.
Basically anytime the mouse would normally change to a finger pointer, that is not active on the first click on a background app.
Admittedly this has its problems especially if you are using two browsers split screen. However imo its designed well because you could do some serious harm by accidentally clicking on something you don't want merely trying to switch between browser windows.