Sorry for the slowish reply... It was a great question and we (Opto 22) discovered that the manual is wrong, so there was some time spent getting to the bottom of it and getting things corrected.....
Ok, from the top....
In a nutshell what we are doing with those values is trying to remove the need to do it in PAC Manager.
We figured that it was a pretty straight forward task, why the need to use two applications when you are downloading to the I/O anyways.
In time you will see more and more of the PAC Manager settings make their way into PAC Control. (PAC Man will never go away, don't panic, we just are allowing things to be done from PAC Control to save the extra step where and when it makes sense).
That was the thinking, so now that you know that, lets keep digging.....
Because the values are 'embedded' in the strategy, they are saved to flash along with the charts etc (assuming you have the 'save to flash' option checked in PAC Control for that strategy).
'Latter restarts' as you call them, will simply be the controller powering up, copying the strategy from Flash to RAM and running the power up chart from Block 0. This will set up the I/O as part of that process, just as it always has done.
(Hint, if you set the values in the strategy and power cycle the controller, you will see the values as they should be in PAC Manager - as you would expect, its just a memory map location in the I/O in the end).
The how and why to use them is the same as PAC Manager, but in PAC Control.
The manual is wrong and has been corrected, they are only for Analog Inputs. NOT outputs.
So, in short, where you used to do those two functions in PAC Manager, you can now do them from PAC Control.
On the other hand, if you are comfortable doing them in PAC Manager, then just ignore that new section in PAC Control and keep doing it the way you have (and as you commented, don't forget to save to flash in PAC Man).
If you still have questions, just ask, we have really appreciated your post, this sort of feedback is really helpful.