If you pay attention to the info on your diagnostics tablet, then you know exactly what using the right tool on different objects does.
They advance the engineering mini-game. If you've played BaDIK think if it like the mansion game. At the current progression of the story we can start it, but not finish it.
There are several interactions that add new clues to the tablet.
And I've found 2 that will advance the progress %. Example:
The server in the Cistern will advance the software diagnosis to 20%.
And I, mostly, like the addition of 'action points' to the free-roam in the 3rd chapter. Do you want to blow a ton of time on interactions with the characters or do you want do your job (engineer) and solve the power mystery.
My main criticism of the free-roam is that I want a indicator to show how many 'action points' I have before the free-roam ends. It's tricky managing your 'time' properly when you don't have a watch