My biggest difficulty is choosing a language/framework/engine
Which is somewhat ironic, because I know that "sit and just do it" is the ideal start. Think less about choosing, just pick it up and go.
But I end up spending more time looking up things and getting excited about them.
LOVE2D? Oooh, it's lua! It can even run on Android! DragonRuby? Oooh, simple and lightweight and fast! Oh wait, Godot just had a new update! Hey, maybe I should get back to programming Java, libGDX looks neat! Damn, Raylib feels like it does many things right! And on it goes...
I overwhelm myself with choices, start a bit then abandon at the second hard-ish hurdle (like menu/interface showing under the map despite lots of fiddling with the Z position, in Godot). So, yeah, just exposing my problem, I suspect I'm not alone in this.
Your Godot problem sounds like you might have ordered your scene tree wrong. The scene tree reads from top to bottom, so if your interface elements are further up the list than the map, they draw first and then get covered up.
AFAIK, the Z index was supposed to be the definitive thing defining what shows on top of what.
There was also a weird problem where my map would display on top of characters if I moved to tiles in the negative position (x < 0, y < 0), so I had to make the whole map within positive values.
There is a node for Y-sorting in Godot 3, is that what you're thinking of? Y-sorting was rewritten for 4.0, so that node doesn't exist in the latest version.