This is not true.
First of all, you're mixing you're experience as a computer engineer with the creative process of a writer. Because what you're talking about: character traits, scenes, dialogues spoken, lore pieces, interactions... are all elements of the narrative and not of the different programming sides of developing a renpy game.
Nevertheless, those narrative elements could, indeed, be usefully tracked by the game's code. And that's what most game developers do, but not Irphaeus. And that's why I told you, he's not doing it, so it can't be an excuse to say developing is growing more complex. In any case, the great complexity of tracking such things comes down to setting a variable to a boolean value. That's it.
What can be difficult is to know and remember when, how many and in which way use all those variables. But that is a problem of the literary development. And yes, as you practice more and more you learn to handle those things more effectively.
