Yes, a misunderstanding. I assumed you had only single phase power. I guess it’s all those electric saunas in Finland needing three phase
Okay, you’re inputting 400vac 3 phase into the drive with the expected 540 volts on the dc bus. The drive can output 400 volts by design. It is only the motor parameters that is limiting the output voltage.
So, two issues as I see things but neither should be cause to stop your effort, at least short term.
1) You will not have sufficient drive output current to run the motor at full load, you should have 50-60% of the motor rating. Drives are current rated devices, not power rated. That means the output rating of 1.1KW is based on a 400v output, not 230v.
2) The motor may fail prematurely, long term. Single phase motors are generally speaking, not designed for PWM supplies. Failure could be days, weeks, months, absolutely no way to predict this.
The failure is in the insulation system of the stator windings, almost always happening in the exposed end turn loops of the stator windings. With the 400v mains and the resulting ~550 v dc bus, the motor can experience very short duration voltage spikes that are 2 times the bus voltage. This is know as standing wave. Motors that are “vfd ready” or similar marketing terms have higher voltage withstand insulation of the stator wire. If you had a single phase input vfd, this voltage stress would be only 650v rather than the 1100v that will happen with the higher drive input voltage. A filter can be used to limit the voltage, Danfoss lists these on pages 24/25 of the guide you linked. A dU/dt filter will limit the voltage peaks, a sine filter will remove all dU/dt and all or most of the PWM waveform, reducing the running temperature of the motor. The problem will be the cost for these filters unless you can find something used or build something yourself.
With regard to the phase missing alarm. You may be able to fake the drive out with a resistor in the missing phase. The question will be how much current is required. You might be back to starting point with the overall effect being zero net energy savings.
Did you ask Danfoss if the firmware in the drive could be updated to a version that supports the disabling of the phase loss? That’s a long shot but if you don’t ask, the answer is no.
Sorry for the wall of text. VFD’s appear simple. They would be if the output was pure sinusoidal.