Take a look at my post referenced above. That's basically what they're already doing - they take L1-N, L2-N, and L3-N voltages, attach them each to the "sub-chargers" that feed a common DC bus.
We are talking semantics here. I agree that the 3 phases are combined into a common DC bus, but is that bus the output to the battery, or is it an internal bus in the charger? Because 50/60 Hz transformers are large and expensive compared to high frequency transformers, combined with the fact that high frequency power transistors have become common and cost-effective, almost all modern power supply/charger designs use a flow that is similar to:
AC Input -> DC Rectifier -> Filter ->
Unregulated DC -> High Frequency Inverter ->
High Frequency Transformer -> Rectifier -> Filter -> Regulated DC Output
The regulation/current control is done at the High Frequency Inverter. High Frequency here for power conversion is usually in the range of 40 kHz to 1,000 kHz (1 MHz). Because the frequencies in the second stage are so much higher than 50/60 Hz, the transformers and filters are much, much smaller.
If I were designing the 3-phase charger for Europe, the most likely choice would be to keep most of the charger the same as the single phase North American model, and only change the DC Rectifier and Input Filter. A secondary advantage is that the filtering needed for the Unregulated DC intermediate bus is much less with a 3-phase input. See
Diode bridge - Wikipedia, the free encyclopedia for a comparison of full-wave single phase and poly phase rectification. Using most of an existing design, replacing part of it with a simpler, more-efficient alternative, seems much more attractive than designing a new, 1/3 power design, and stuffing 3 of those into the same space.
Of course, an argument for multiple sub-chargers would be that it is easier to create a charger that minimizes input current harmonic distortion. As Tesla goes to 10 and 20 kW level AC input in residential locations, THD on the AC power lines becomes a big concern. See
"Harmonic Distortion of the AC Power Line" for reference. Given the the battery itself is a big filter, perhaps Tesla have gone out of its way to build chargers that appear as a resistive load to minimize THD issues on the grid. Given that we have heard few complaints in this area, that may be very likely.
Until someone dissects a European charger or Tesla publishes something, we won't know the details of their design, and can only speculate.