I am wondering if this tool might help me speed out my solo indie dev workflow with Godot but Godot already offers 2d bones,  image scaling, tweens and the ability to code shaders for enhanced visual effects so what would you say presents the most value in PixelOver ?

Mostly it will be useful to create static images from these so it's less computation for 2D games, same if you want to add 3D elements in 2D games it will help.
Honestly setup bones in Godot is quite painful in PixelOver it's more straightforward. It's because Godot tools are designed to use them in a realtime game while in PixelOver they are more focused to create assets.
But yes theorically you can make everything directly in Godot. But at least if you want you can try the demo there are some example projects so you can have an overview of the functionalities.