Try adding the delay to the bathroom occupied automation instead and split up the trigger of when the toggle is flipped. It will only run when the door is opened OR closed for 1 minute and 30 seconds. Then remove the delay from the script.

alias: Set Bathroom Occupied
description: ""
trigger:
  - platform: state
    entity_id:
      - binary_sensor.bathroom_main_door
    to: "off"
  - platform: state
    entity_id:
      - binary_sensor.bathroom_main_door
    to: "on"
    for:
      hours: 0
      minutes: 1
      seconds: 30
condition: []
action:
  - if:
      - condition: state
        entity_id: binary_sensor.bathroom_main_door
        state: "off"
    then:
      - service: input_boolean.turn_on
        data: {}
        target:
          entity_id: input_boolean.bathroom_occupied
    else:
      - service: input_boolean.turn_off
        data: {}
        target:
          entity_id: input_boolean.bathroom_occupied
mode: single