Hi,
I've stumbled upon this issue too. What worked for me:
1) find PoE config file under: ~/.config/unity3d/Obsidian Entertainment/Pillars of Eternity/prefs
2) do a backup
3) find and modify to following lines accordingly inside that file:
<pref name="Screenmanager Is Fullscreen mode" type="int">0</pref> <pref name="Screenmanager Resolution Height" type="int">900</pref> <pref name="Screenmanager Resolution Width" type="int">1600</pref> <pref name="_currentDisplayMode" type="int">3</pref>
I'm using the latest version from GOG: 1.0.3.0530
If you need my config file (although I've started from an empty one) just PM me.