It's not so much the existence of the flag, itself, but rather using an if-statement at the deepest-level of the call stack to conditionally modify behavior.

This talk gives a great overview of why boolean flags (rather, if-statements) can be a code smell: https://www.youtube.com/watch?v=4F72VULWFvc

OP's blogpost advocates for data-oriented design (e.g. Entity Component Systems) as a mechanism for avoiding this, whereas the talk I've linked advocates for OOP. Both mechanisms are equally valid (imho) and are inline with widely-adopted industry practices for software architecture.