Windows aren't quite maximized when opened
As a recent Mac convert, I completely feel the pain of unmaximized windows. I get why this works for some, especially long time Mac users and never-did-Windows folks. But for me, this was a serious pain, along with all the other nuances I've been suffering through during an incredibly busy work season as well. 

I just discovered an app called GreenOrbmax, which basically reworks the green + button in a window to make it maximize, in the same manner in which I was accustomed to in Windows.

This might not be the solution you desire - if you find one, please post it, because I'm in. But this seems to be a reasonable solution for now, and since you didn't specify what 3rd party app you were using, I thought I'd share it with you.

Note: it does not seem to maximize Preview windows 100%.