Launching parameters for FTL?
Solution 1:
This may help you.
I hope you know how to use AutoHotkey scripts, or you may have to get lucky/ask another question with more information.
The PC Gaming Wiki also prescribes borderless fullscreen settings.ini changes that may work:
fullscreen=0
lastFullScreen=0
manual=1
screen_x=your x value screen resolution
screen_y=your y value screen resolution
windowed=1
stretched=1