So, the game was always meant to be a Sandbox, but it also has a story to be told. It is much more efficient and easy to lay out a linear prologue with all the important story beats before letting the player run wild, or the sandbox world could feel shallow, confusing or restrictive depending on the approach. I assume other devs do it for the same reason. Even big games, like Kingdom Come Deliverance, are structured exactly like that.
I guess my prologue was big enough that people felt tricked into thinking it was a kinetic novel, but be assured, the full story's scope would be almost impossible to be told well linearly :P. That's why it's such a big prologue.