Disable VSync in Project Settings > Display > Window > V-Sync Mode: "Disabled", if you need a fps cap consider using Project Settings > Application > Run > Max FPS instead
I learned this from developing a game that needs a transparent background. It was from a person named KitzuGG.
Regarding the black box issue. I believe this is due to a recent change in Godot. I encountered a similar issue, and switching from Forward+ to Compatibility rendering mode resolved it. However, be aware that Compatibility mode comes with some drawbacks.
