Cowbell, please push this issue up to Tesla HQ - because we also ordered our S 100D with the standard 48A charger, with the expectation that we could upgrade to 72A later.
When we placed our configuration (I took a snapshot of the configuration page), it clearly states that the 72A upgrade was $1500 if configured with the car or $1900 if configured after delivery. If that future upgrade option had not been available, we would likely have purchased the 72A charger with the car.
However...
We've had our S 100D since March and have almost 18,000 miles on it. We're using an HPWC on a 100A circuit that is limited to 48A charging due to the onboard charger.
And we've been able to get a full charge at home overnight since we've got the car - so, for at least home charging, we really don't need more than 48A.
Destination charging is a different matter. When on a road trip, we'll always try to stay at a hotel with a destination charger. Some destination chargers are on 100A circuits and can support up to 80A charging - though most we've encountered seem to provide less, probably 50A. For overnight charging, the 48A charger has been fast enough - and what most of the destination chargers currently support. For those few 80A chargers we've found, a 72A onboard charger would be nice, but unless you're trying to get a faster charge during the day, 48A should be enough for overnight destination charging.
The onboard charger isn't used for supercharging, so it doesn't matter if you have a 48A or 72A onboard charger, the supercharging circuit bypasses the onboard charger.
So that gets back to our original decision. If 48A is enough for overnight charging, and we would only need a 72A charger for during the day charging at a destination charger that supports 80A, would we use that enough to justify spending $1500 (with the original order) or $1900 (if Tesla provided the upgrade)?
At least for us, the answer still seems to be no. Unless you do a lot of charging during the day - for overnight charging 48A seems to be enough, at least with a 100 KWhr battery pack.