I have Pillars of Eternity (2.01 - Linux - GOG) configured to start in full-screen mode at my monitor native resolution of 1920x1200. About 70% of the time Pillars of Eternity starts in windowed mode. (At 1920x1200 this means some of the bottom is cut off due to the window frame.)
A quick fix that works every time is to enter the Pillars of Eternity graphics configuration window, un-check the full screen box, hit apply, then re-check full screen box and hit apply again: Now in full-screen mode.
All other graphics work without issue.
Attached is Player.log from
~/.config/unity3d/Obsidian Entertainment/Pillars of Eternity