According to bricklink, 88003 is the **set** containing exactly one **part**, namely the 99499 motor.
You can buy the motor as a set in lego shops or online, it's packaged in a plastic bag, which probably accounts for the 3 gram weight difference between the items.

To my knowledge there are no different versions of the powerfunctions L motor.

Here is the list of the sets the motor appears in, note that 88003 is listed as well:
https://www.bricklink.com/catalogItemIn.asp?P=99499c01&in=S