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.
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.
Found this aquatic fungus a couple weeks ago (Vibrissea truncorum) (mander.xyz)
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....