Your wiring shows one of many possible arrangements of switches and inputs.
The PMDX-416 has 5 isolated inputs and 3 non-isolated inputs. When you
connect something to the non-isolated inputs that will tie the non-isolated
ground to the ground of the machine, then you have defeated the isolation
between the board and the machine. On a table top machine this is not a
big deal as long as you do not have ground loops. For larger machines I
would recommend avoiding having the non-isolated ground connected to
the machine. In your case, it is the wire or clip lead to the cutting tool
that will tie the non-isolated ground to the machine through its spindle
bearings. This is a connection that will exist only as long as the clip lead
is in place, so it is less critical with respect to picking up noise such as
from a spindle with brushes or driven by a VFD.
Your diagram shows all switches as normally open. Mach4 can be configured
to accept either normally open or normally closed switches, but in the case
of your three limit switches wired in parallel, they must be normally open.
If you had three normally closed limit switches, they would need to be
wired in series.
Standard practice for an E-Stop is to make it normally closed. This is so that
its wiring is fail safe, i.e. a broken wire will cause an E-Stop condition.
You have used individual home switch inputs. This is nice to have, but you
should be aware that Mach4 will allow home switches to share a single
input. The drawback is that Mach4 will not be able to tell you which axis
is parked on a home switch if you should power up Mach4 while a home
switch is active. Combining home switches could give you a free input
for some other purpose.
When combining switches on a single input, you tell Mach4 what you are
doing by entering the same input data in each row of the Input Signals
configuration chart for each switch function that shares the input.