I recommend that you disconnect the high leg phase of the open delta POCO supply, which is easy to identify from its higher L-G voltage. And connect the VFD directly without going through a transformer.
The worst choice would be to use the two wires that you measured with the lowest L-L voltage on an averaging meter in your post quoted below. I highly suspect that this voltage is across the "open jaw" of the two open delta transformers. I believe that a third harmonic is reducing the average but increasing the peak of the voltage above that of a sinusoid, while still maintaining an RMS value very close to the other two L-L pairs.
The slightly higher average measurement that's above the RMS on the other two L-L pairs is likely from a third harmonic that flattens the peak voltage but boosts up the "sides" around this peak. A flattened peak voltage could possibly reduce the peak current through the rectifier diodes, which would not be a bad thing.
" This is the problem unit:
Averaging meter
Input, 125,125,217, 250,250,226
...
True rms
Input 123, 123, 215
246, 247, 248"