Thinking a bit outside of the box:
Your power company will provide single phase service. You also want to use a generator.
Your preference (stated from the beginning) is to wire the structure for 3 phase, use the 3 phase generator directly and have some way to convert the POCO supplied single phase to 3 phase.
But you are willing to consider wiring the structure for single phase, and running the generator single phase.
This tells me that you don't have any 3 phase loads, you just want the whole building as a 3 phase load to match your generator.
How about wiring the building single phase, but as three separate 120/240V 200A 'systems'. All three of these are supplied from the POCO 120/240V split phase, but when transferred to generator power they are on separate phases.
-Jon