You have 1 system that works installed as drawn in post #99.
You have 1 system that doesn't work but has the incorrect transformer.
What you do next depends on what the HVAC equipment manufacturer and the transformer manufacturer tell you.
If the HVAC equipment manufacturer tells you that the VFD can be supplied with balanced 240V single phase, then you could just run the two 'base' legs from your high leg service to the VFD and be happy. If the HVAC equipment manufacturer tells you that the VFD needs balanced 3 phase, then you _must_ use the transformer.
IMHO you should continue down the route of getting the transformer supplier to correct their mistake sending you the wrong transformer, and reserve the '2 legs' approach as backup, and again only if the HVAC equipment manufacturer gives their blessing.
