Hey there, glad you enjoy the art!
I'm not a Godot user myself, so I was unaware of the limitation... But yes, my more recent tileset spritesheets are indeed grid-aligned and should be easier to use (example). This tileset's spritesheet was done with an older workflow. I can do an update soon to make the spritesheet format more similar to the new style. Thanks for the feedback and info about Godot!