Do you suppose they use the smaller charger because of the battery warranty? It's not going to make much difference if you charge occasionally at a higher rate when on a longer trip but if you doubled the charge rate every time you charged for the life of the battery that might have an adverse effect. Even with 650 watts it will always charge overnight. Are they protecting us from ourselves maybe?
Purely a cost concern. Aftermarket chargers run $600+ for 3.3kw, now imagine a nice OEM unit, like the 6.6kw charge tank, it cost 2.3k. They certainly could price the fx/s/e a few grand more, but then why not buy a beefier model?
Gotta remember too that those cheap chinese chargers don't meet US emissions regulations, and Zero has to meet those as a manufacturer. They had to develop their own 3kW charger with a 3rd party, and it's too big to fit on an FX in the same spot. Plus the J1772 inlet is larger too. So that's a new frame too.
The FX was designed many years ago, and chargers weren't nearly as small and efficient then. If you ask me, in the next 2-3 years we'l see everything that's not based on the SRF tech get replaced with an SRF variant. S/DS/DSR/SR/FX all will get replaced. That reduces the number of parts, updates the screen and app, improves charging, and gives them the greatest return on investment.