If you care more about being able to see the quest text and you can live with a grid in the top right corner of the screen, just don't replace that one file. Somehow, whether or not the quest text is visible depends on the opacity of that 1x1 px file. Replacing it with a blank texture removed the grid from the hud, but also removed text shown in the quests menu.
Also, a 1x1 px white square texture in the game is used to draw the map grid on the mini map. Removing it also removed the map entirely, making it difficult to go to a specific save spot in a level or to know which areas of the map you haven't explored yet. To access this feature, refer to the FNA user documentation. The light bar will change to Dust's color and will change colors when using the Dust Storm as well as when leveling up. Warning: This mod has side effects which make the game more challenging. Dust: AET for Linux supports the DualShock 4 light bar. Make the hud as small as possible and move it as far to the sides as possible to move the remaining hud pieces out of frame. To remove the rest, go into your game Settings and Hud Options. Now, when you start your game, your hud will be partially invisible. Unpack this zip file into your Dust installation directory and overwrite files when prompted (again, make sure you backup your content folder before doing this). Back up the 'content' directory in your Dust folder.