Rather than address any of the specific questions raised about what runs before whatever, which as I mentioned, I could not be sure of anyway, can we look at what is being attempted - from an overall view?
It seems to me that you want a live session to be launched with some specific changes made to the released ISO.
As you mentioned, using persistence is not suitable because you want no other changes to be able to be made to your 'install'.
The next means of achieving this, that comes to mind, is a remaster of the changed system, so that the ISO contains your specific changes at every boot.
This might not be suitable either, if for instance you have a lot of different scripts you might wish to run to give different results.
On the other hand, if you do not have multiple different scripts, then it would appear to be the best option. It is simply done, and if in time, you had some changes to make to your script, it is a simple matter to remaster again, to produce a new set up.
In addition, if you only have two or three different set ups you wish to choose from, then it is possible to have a separate 'install' for each (via remaster) and put all three on a LiveUSB device.
I understand this post is not addressing your questions, but instead I am trying to address your needs, and find a reasonable solution to them.
It appears that whatever you are trying to change is already loaded from the ISO (loaded into memory) before the script runs, and therefore those things would need to be unloaded or overwritten by the changes, to allow those changes to be applied.
Persistence is the only way I have used to achieve that.
Other than persistence, a remaster will make the changes permanent ..... with the option to boot a different 'install' for different set ups.
Maybe some of the above will help .......