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See the light blue star on your screenshot?
That is active offsets.
In Axis GUI you can choose to show offsets, i do not use Probe Basic so i do not know how to show them.

Standard would be the normal TB6600 and above up to huge servo drives, self contained in a box for each axis.
The 3D printer ones or step sticks are ... well for 3D printers, useless without their respective boards, very prone to interference, and some will just fail by touching them at certain conditions. Yes, TMC are pretty good, but using stealth chop or another such feature (forgot the name) is clearly stated to cause small positioning errors, so for anything vaguely precise should be avoided or used without those features active.
As luck would have it, there are step sticks with TB67S109 chips, i have some, found out i never need to push 3.5A on a 3D printer!

I don't follow. I have no offsets in use.

I don't have homing switches on this machine, it homes off absolute encoders from the servos. But I don't see why that matters here? The machine is homed and G53 is properly referenced to all the axis limits. The work envelope displayed is correct, as is the location of the tool within the work envelope. G54 is my work offset and is in an arbitrary position in the center of my work envelope (middle of the air here for testing code). The code I loaded is being mapped onto the G53 origin rather than the G54 origin that the code is calling and the machine has active.

Code should always respect the correct origin called, G54 in this case.

Does the machine have home switches?
If yes, home the machine then touch off each axis/joint in G54.
There are active offsets in use, remove those first, see if that puts things where they should be.