In addition to PrintScreen, there are other "default" actions provided in Settings > Shortcuts > Custom Shortcuts as shown in the image below:

PrintScreen opens the Spectacle GUI. If the application is already open but in the background or minimized, pressing PrintScreen doesn't bring the GUI back into focus or above other windows. As you noted, you'll need bring it to the front yourself.
If you want to take a full screen screenshot, instead of PrintScreen, use Shift+PrintScreen to immediately do so without invoking the Spectacle GUI.
Similarly, Control+Shift+PrintScreen lets you immediately screenshot the active window.
The fourth default option available is Meta+Control+PrintScreen if you want to select a particular area of the screen.
As you can see, if you want to carry out any of the options in 2, 3, or 4, you don't need to press just PrintScreen and then have to deal with Spectacle's GUI. The three options execute immediately without invoking Spectacle's GUI.
However, if you want to do something not covered by the three actions described above, you will need to use PrintScreen and Spectacle's GUI. Typical cases would be taking a delayed screenshot and wanting to include or exclude the mouse pointer.
Your Spectacle settings are saved in ~/.config/spectaclerc but it's advisable not to edit this file directly. Instead, use Spectacle's GUI where possible.
I'm guessing from
Can I make application activated on PrintScreen button?
that when you press PrintScreen, you want Spectacle to be focused if it is already open (but minimized). And if it isn't running, you want it to start when you press PrintScreen.
If you install wmctrl (available in the Universe repository), you can use
wmctrl -xa spectacle.spectacle || spectacle -g
as a shortcut. This command checks to see if Spectacle is running: if it is running, the Spectacle GUI is brought into focus. If Spectacle is not running, the command launches Spectacle.
If that is indeed what you want, make a new custom shortcut with Print as the trigger and the code above as the action. You'll be warned that there is a conflict and you'll be asked if you want to reassign the function. Do so.