Judging from the paths, it looks like you are not using the Itch client; the Itch client will automatically "install" the game in directory names that match the "project" and your paths don't match.  Example: If you use the Itch client to install Maelstrom in C:\Maelstrom, you would see a C:\Maelstrom\gentlemen-of-fortune-maelstrom-engine directory that will contain the DirectX9_64bit directory. So it looks like you downloaded with a browser or something and extracted a .zip file?  If so, keep in mind that you won't get automatic updates and will always need to check for updates and download the entire thing, every update; the Itch client will update only what has changed and will not download the whole thing.

In any case, to run Config.exe for the resolution, you can copy that same shortcut that you show.  Copy and past the shortcut, then modify the shortcut name to Config COAS.  Edit the properties by changing the Target by replacing Maelstrom.exe with Config.exe, add a space, then copy/paste the Start In to the end (with the double quotes):  C:\Maelstrom\DirectX9_64bit\Config.exe "C:\Maelstrom\Games\GOF City of ships"

Remove the Start In value, or replace with Start In: C:\Maelstrom\DirectX9_64bit  Either way should work.

Quick summary:

Target: C:\Maelstrom\DirectX9_64bit\Config.exe "C:\Maelstrom\Games\GOF City of ships"

Start In: C:\Maelstrom\DirectX9_64bit

Launch the shortcut, change the resolution, Save and launch game.  If you want to config a different game, like GOF or ERAS, you will need a different shortcut, to the same Config.exe, but change the trailing "C:\Maelstrom\Games\GOF City of ships" to the path of the other "mod."