I wouldn't be able to compare them from a feature perspective, but it seems like Flutter itself is a cross platform general 2D app development toolkit, and people have used it to make games despite that not being its focus.

This Flutter Casual Games Toolkit looks to be a layer on top of Flutter to make that easier to do. Which is as reasonable a reason as any to create a toolkit like this.

But Godot as an engine predates the release of Flutter. So I would imagine starting fresh with no Flutter experience or jumping from Unity you would be probably better off with Godot.