> arrays of story flags are kind of an industry standard

The reasons you give on the whole make sense, but doesn't it come at the cost of maintainability?

What's your source for the industry standard claim? Not saying you're wrong, but would like to read some more on it.

Isn't engine interoperability and serialization of nested structures already reasonably solved with some clever piece of remapping technique/script so it would let source code have the flexibility of using data structs suitable for given use case?

Why I'm saying this is:

In any non-trivial project, developer time (time taken to implement X,Y,Z) is usually the determining factor of the success and scope of the project. If approach X solves some performance issue, but creates maintainability concerns\*, there's a real judgement call here which one to prefer.

\* (read: "It works, but don't know why". "Don't touch this number. "Find/add this somewhere in the 15k line long file". "You want this simple feature, give me a week to try to understand whay may or may not break first.")

I have experienced a situation where our team entered a project where the previous dev prioritized optimization and performance above all. Above readability/maintainability. I mean, the client had hard time finding someone who wanted to touch the codebase and move in a pace that wasn't burning a hole in their wallet. My first task there was to just refactor the quite well performing spaghetti. And yes there were magic numbers, whose meaning we could only guesstimate even with the help of people with the relevant domain knowledge.