I'm assuming that the risk is that since only one phase is being used to supply all the output power, that it is the rectifier diodes on the one input that risk being over-loaded - all the output power being derived from one phase set of rectifier diodes rather than three ?
True, but since the rectifier diodes are usually integrated with the rest of the power devices, there's virtually no cost to the manufacturer to make the devices very robust (i.e. to use the same spec devices for the smallest and largest power VFD in a range).

The only real issue is ripple current heating in the capacitors.

Bill