Amazing ! You're insane and bold with this 3D code you've done. I wonder why not making fake 3D like in the old days of 8bits computer ?
It's great also to get some such insight of dev process, as game dev myself, it's good to know how others do their games.
To conclude, I believe you would have lost a great deal of time with Godot, because the usual drawback of these engines is always it make thing complicated easy, but easy thing complicated. For instance, adjusting container sizes for UI took more time than just coding a (not so) basic game at all.