I'm not sure exactly what the difference is, but I note that in the nav retrofit instructions it says:

E46: "In cars with a BMW Business CD radio up to 09/01 and in all other cars up to 03/01, the aerial booster (1) must be replaced by an aerial booster (1) for cars from 09/01 or 03/01 onwards, respectively."

E39: "Cars built before 09/00 only:
Unfasten the aerial cables (1) from the aerial amplifier (2) and tie them back.
Exchange the aerial amplifier (2) for the version after 09/00."
and
"In cars built before 09/00 the aerial amplifier must be exchanged with an aerial amplifier for cars built from 09/00 onwards."

E38: "The existing aerial amplifier must be replaced with the aerial amplifier (part No. 65 25 6 906 082) for new generation on-board monitor radios"


All dates etc coincide with the change from OG to NG radios.

I don't have the retro-fit instructions for the E39 Touring but it will be the same.
The difference in the antenna amps is the diversity control - the switching between the 3 x FM aerials fitted to your car according to the strength of the FM signals. The radio tells the amplifier which antenna to use, and the aerial amplifier switches the antennas.

This is very important for good FM reception, and the impact on a Touring is very different to the impact on a Saloon due to the totally different antenna design on the Touring (side windows vs rear window)

Jochen