There is an ongoing problem with the terminology used to describe the functions of the MEMS 2J.
I am no expert, but information is available in the Haynes manual on Engine Management and Fuel Injection. It has a section on MEMS and although it covers the entire MEMS range, it can be used to understand its functions.
When the ignition is turned off the stepper(IACV) is moved to the fully closed postion, then moved to a postion where the throttle plate is slightly open, ready for the next engine start. This happens no matter how long the key is on/off and without regard to pressing the throttle. Resetting the stepper so that it is in range, requires the use of the scan tool(FCR), T4, ACR or other tool. The adaptive idle measurements are retained in non-volatile memory and cannot be lost - even if the vehicle battery is removed.
I don't think there is a standard usage for the term indexing and resetting as it is not really defined in any of the manuals.
Use the tool to check the status of the steps and readjust only if necessary. In one of the sections of the Rover documentation, it indicates that a value of 20-40 is acceptable. The ACR adjusts this to a tighter specification.