Well, I don't know why that would affect anything having to do with backlash. All Mach does is provide the trajectory plan to get from the start position to the end position of the move. The plan should never change just like the distance between your door and your mailbox never changes. How you get from your door to your mailbox is the motion controller's job.
As to Cycle Stop. I don't like it because it is not recoverable. My YASNAC control that was on my Matsuura mill had Cycle Start, Reset, Feed Hold, and an e-stop button. If I wanted to stop the machine and walk away for a bit, I hit feed hold. On my YASNAC control, Feed Hold was a yellow button. On most Fanucs, it is a red button but it is labeled "Feed Hold". I kind of like the red button because most people associate red with stop. Neither has a Cycle Stop button. When I converted my mill from YASNAC to Mach 4, it still has no Cycle Stop Button. Not on the panel and not on the screen. I believe this is correct for for most milling applications. I'm not a lathe or grinder guy, so I just don't know. But a Cycle Stop button has been a Mach feature for nearly 25 years now and people just expect it to be there, for better or worse. Worse, IMHO.
But anyway, pressing cycle stop USED to be semi-recoverable on Mach 3. But with Mach 4 and its' MACRO B, better cutter comp, and more advanced Fanuc compatible interpreter, Cycle Stop is just not recoverable. Especially if you are using cutter comp. You need to use "Run From Here" to restore the state of the machine to restart. If you don't use cutter comp or Macro B, you may be able to get away with just pressing Cycle Start. But your mileage may vary.
Steve