I know nothing about MySQL, I am sorry.
You don't need Scons for the upcoming Godot Extensions (the successor of GDNative in Godot 4). Documentation isn't yet complete, but there's an example of how to do it (that actually worked under beta 4). But in the end you just compile your project independently from the Godot engine (well, you need the headers of course).
I find Godot 4 beta too buggy, and there's still the danger of breaking changes, to actually do productive stuff with it atm and on that level.