I just used my knopp tester (wiggy to use slang) No digital or multi tester.
Two questions:
First: how is this not a grounded system if a ground wire is ran from the panel to the transformer, to the disconnect and to the machine?
Second: How does 250.20(B) apply since it mentions 3-phase, 4-wire, but I have 3-wire on the primary and the secondary, no neutral for both? Is it considered a 3-phase, 4-wire system since the panel it comes from is 3-phase, 4-wire, wye?
Grounding the transformer shell does not make the secondary side a grounded system. It takes a ground connection to one of the windings to make it grounded.
If you do not ground any of the X terminals, including X0, nor any of the wires connected to them, you will measure zero volts from any of them to ground. There is no return path to allow current to flow through the meter. (Yes, there is current through a voltmeter! But it is a smaller current for a high impedance meter.)
If the voltmeter current is small enough, then the capacitance to ground of the other words, including the transformer windings, will carry enough current to allow a meter reading close to the nominal voltage.
If there is an X0 terminal on the transformer secondary, it is a four wire wye system. But if there are only line to line loads it may not be required to run that fourth wire anywhere last the transformer.