So having been in contact with Greg, the following has become clear:
The LPT has a different behaviour when the limits are tripped to how the SS handles them. He is aware of the difference and he has the fix on his list but not a priority.
Greg modified the plugin to fix the issue I was having with the e-stop being declared when the limits were hit too. So BIG UP TO THE MAN!
Most of this thread has been to try gain an understanding on how the SS differs from the LPT. Hopefully, it will help others that are making the switch.
Jeff, thanks for sticking with it too.
Now, does anybody have a video of the SS working with backlash compensation? It seems that mine is working when I compare the Mach DRO and the physical DRO on my machine but I do not get the jerk with the change in direction that I have come to know from the LPT.