Bug: SC2 Graphical settings aren't saving; Settings aren't inherited from the install

[Slimurgical]

What happened?

When starting a mission, the game does not inherit settings values from Variables.txt in the Starcraft 2 documents folder, and it does not retain any changes to the Window state. You can change it however is wanted and it will revert to windowstate=1 aka Fullscreen (Windowed). This requires any player who requires Windowed mode to have to change the state upon beginning a mission. Other settings are saved, namely Hotkey profiles, but graphical setting changes are not.
Note: If this is intended functionality (don't know why it would be) I would at the least like to know what file Archipelago pulls config details from with Starcraft 2.

What were the expected results?

When the game is started, it retains any and all values set in Variables.txt as well as changing them when changes are made, even if Archipelago is creating its own config file for the SC2 game window, the expected result is to not have it reset the window mode everytime the window opens, to instead have it save to whichever file Archipelago is pulling config details from. The expected result is that thep layer doesn't need to manually set it to windowed each time no matter the ease of the method one uses for it.

Software

While playing

[neocerber]

@Ziktofel could you look into that?