Not true. Marlin ignores the state of the endstops unless you are homing. You can enable this feature, but we leave it off so you don’t accidentally ruin a job if a wire comes loose, or a switch gets bumped. You really can’t hurt anything by running into the endstops by accident.
I don’t know what to tell you about the homing sequence though. As long as the endstops are connected in the right spot, and they register correctly in M119, they work. That’s been my experience.
I would like to know more about it though. I am not shutting you down, I am just out of ideas.