I've half-learned both. My impression is that Godot is more like a framework (but more so) with prescribed ways of doing things, with lots of custom languages and formats, and Heaps is more like a library you use in a codebase that belongs to you a bit more.

From an ability-to-ship-games perspective, starting out, I'd go with Godot. Putting together a game's architecture from scratch with a library like Heaps sounds like a fun project, but to just get a game out the door without fussing around, Godot makes things easier without major downsides. Godot has so many custom things because those things work.

That said, I'm just a dabbler, so I'm sure other people will chime in as well. I'm also sure that if you invest time in learning Godot or Heaps, it will pay off well, because they are both mature projects that people have used to ship commercial games.