Whenever the game asks "You are about to embark on a long distance journey, skip directly to destination?" choose NO to get there manually. There's your free play right there. iirc your first chance is right after you pick up Greyhair. You can also detour as soon as you've replaced the pirate ship.

If those instances are too early for you, wait until the Precursor mission arc: when you reach X203 grab Joseph and instead of proceeding to the rendezvous point, backtrack to X297 and from there it's free play.

Scripted auto-destruction happens when you're in the middle of a mission or at the end of the game. But by the end game I've had my fill of roaming around already so I'd rather just get the story over with. There's no real point to "free play" anyway since other than looting and training, there's little to do once you've toured the place and exhausted the secrets.