Are there any difference between the Power Functions 88003 and 99499 L motors?
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 Power Functions 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&amp;in=S