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No, unfortunately there isn't anything you can do about this. The first line will give you max number of digits.
The limiting factor is Ethercat's use of 32-bit float. Hal already uses 64-bit float.

If you in some way could increase number of digits from the encoder over Ethercat. That is, to make Ethercat use 64-bit floats for the encoder position, then the second line is the one to use, that will give 64-bit float in to hal.
But it usually isn't possible to increase to 64-bit output, only if you have exceptional control over the device like it is something you make yourself.

I am a router guy and what i am doing is not recommended by anyone with an actual mill but is close enough for me. (Er20 router non-repeatable)

The spring on my tool setter is reasonably soft so it is able to trigger before my probe would.

So for each time i run / change jobs i load my Probe but don't connect it (tool 99) Probe the length of the tool setter just like it is any other tool. 
Then connect probe and probe xyz as needed using the standard probe basic probe screen.  At this stage the system now knows xyz of what is my stock.
Then change to what ever tool is needed for the job and probe that length. It calculates the difference between and off we go.

I find that i am within .01 - 0.03 mm using this method and for a router on Aluminum this close enough for my needs. 

The tool change i use is based off  GitHub - TooTall18T/tool_length_probe: Tool length probe subroutine for Probe Basic.  and V3.0 if you have upgraded to the latest probe basic you may need something slightly different.  It seems to work for me still in the latest build of probe basic but i have done a number of customizations that i need to un-do to get back to standard  

I really need to do a new video.

The forum starts here
www.forum.linuxcnc.org/18-computer/44828...ard?start=630#263406

And the following video shows how to flash the ST-Link. Note the firmware you will need is not that one used in the video.