Gantry configuration example different

  I have read different gantry kinematic configuration. Is there a technical different  for this two example? and 

yes both lets you use in joint mode before homing when it changes to cartesian coords

I think I prefer homing on startup so often leave the both out

Thank you,
and do you know the different between this parameter. Is there any other handle from the motion planer?​​​​​​​ and

There should not be any functional difference.
This field is the only thing that maps the joints (motors) to axes.
Note that pncconf and stepconf configure your hal file signals in terms of  x, x1, z, z1 etc.
I found this very confusing if you did remap the joints.

I rewrote my hal file to use joint numbers for signal names back when the 7i76e was not supported by pncconf so it was hardcoded anyway.
My current build uses ethercat hardware which also required hand coded config files so it is numbered in ethercat slave order (0,1,2).
I think this is how it should be done and stepconf/pncconf behaviour is a carry over from before the independent code was released in v 2.8.
I did suggest it should be changed back then but lost the argument.
 

This I want to know. It is not important for the motion planer.
In compare to fanuc control are the main axis first and the slave axis at last. So are the combination XYZYZ one argument. But in config, reading is the XYYZZ easier. All joint after one by one. 
If I want to add an axis, are the other easier. But usually should the axis number clear before I start to build. 
In the end, philosophical option...

The planner is working in a XYZ space so it does not care about the joints and where they are used.
A robot arm might be a bit different.