True, but you probably won't be actively working in some other app when that happens. Your hands were, up until that point, actively involved in connecting the phone to the laptop. It's still a bit annoying - maybe you only wanted to plug in the phone in order to charge it. But I'd say for that moment, the phone is your focus, and the pop-up app is related to that.
For each new phone. It's beyond annoying and can be embarrassing when Photos opens to reveal your colleague's pictures stored on his/her phone. I've learned to open Photos first and hide as much of the application as possible before plugging in a new phone.