Lol I’m trying to digest your post slowly.
I’ll try to go step by step but a couple of things stand out right way.
You did a G0Z100??? (not G0Z-100???)
G0Z100 should make the motors move the printer up and not down. This is an indication that all steppers are inverted. Check setting $3. If $3=0 change to $3=7. if $3=7 change to $3=0
You also may need to do the same on $23 (homing direction invert mask) the same way.
Positive Z should make the printer go up and negative Z should make the printer go down.
NOTE: Ov:100,100,100 are the overrides rapid feed, normal feed and spindle (not distances)
Yes confirm with a ruler. The output of the WCO is were the machine think it is. Not were it actually is because you don’t have a close feedback system (motors + encoders).
I guess the values presented are relative to the effector and not the base (just a matter of reference I guess). They should apply anyway because we are trying to eval relative motion (from an initial position to the next) and not absolute.
If the total distance matches between the sim and the real displacement on your printer good. That is enough for me to know that no steps are being missed in any form. 
Steps can be missed in several ways. If you exceed the driver or motor capabilities you will ear and see the motor jamming and making noise (high pitch). But if the step signal is somehow unrecognized by the driver you wont notice anything besides not running the distance it should. This should not happen on µCNC since the generated step signal is simetrical for (ton and toff)…but just to make sure I asked you to check it out.
Let’s see if fixing the direction on the steppers also takes care of that inversion. Maybe your mesurments are correct after all.