@incidrthreat
Hi, I have a delta so I'll try to be useful...
The error that is blocking your right probing is this , in "config.g":
Rnnn : Radius to probe

M557 R90 S20 ; define mesh grid

The R parameter MUST be bigger that the value (radius) you set in http://www.escher3d.com/pages/wizards/wizardbed.php bed generator.
Now , as you wrote , they are coincident so they come skipped.
Your radius is 140 so try M557 R120 S20 instead.

Then, cosmetic stuff... I suggest you to erase the G31 line in the config-override and work for the zprobe in config.g for don't make splitted code. And leave geometrical and other auto-calibration in the override.

1)In config-override (remove this line and work in config.g):

; Z probe parameters G31 K0 P500 X0.0 Y0.0 Z-0.31

-What is in G1 "K0" for? in the wiky https://www.reprap.org/wiki/G-code#G31:Set_or_Report_Current_Probe_status it is not mentioned.
I dont know if this can generate errors somewhere. Remove it.
-Try to set "Z-0.1" till you are not certain that all work as it should. Then you'll refine the stuffs.
-P500 . For the smart-effector this line is suggested G31 P100 X0 Y0 Z-0.1. (look at commissioning)
https://duet3d.dozuki.com/Wiki/Smart_effector_and_carriage_adapters_for_delta_printer
https://forum.duet3d.com/topic/16758/g31-trigger-value-what-is-it-good-for?=1641345568624

2)In config.g ,despite it come bypassed by the config-override.g ,change the Z from 5 to Z-0.1. 5 mean to fly too hight for the head.

G31 P500 X0 Y0 Z5

For the smart-effector this must be "P8" not "P5"...

M558 P5 R0.4 C"zprobe.in+zprobe.mod"

For the axis limit set a negative value so that if your Z0 is too high (for some reason) and with babystep you have to go really close the bed , you'll can. Set it ex at Z-0.3.

; Axis Limits M208 Z0 S1 ; set minimum Z

After you made those change to the code:

-power off , power on the printer.
-home (G28)
-run a single probe (G30). (it will be slow)
-keep the right height and write it in the override.g M666 H parameter.
-restart the printer
-run at least 3xG32
-in console type M665 for read the actual value and copy ONLY the R in the ovverride.g. (and leave the M666 to 0 for all the items)
In this way you will leave to the auto-calibration the job to recalculate the other parameters. In my experience if you put too much manual settings and they are not perfect , the result come even worse.
So basically for the M665 you can add manually : rod length , radius (after at least 3 calibration) , height.

It's late here in Italy... I dont' know if there are more errors in your files... but I'll collapse .... try those change and let us know 😀