The second option is using S12Z Flash Programmer instead of "standard programming". It is a bit slower but offers almost full control on the programming procedure. You have to show a new window with "Target Tasks" that is a bit hidden under "Other..." option.
RadekS_1-1698923372358.png
From that point is rather pretty much straigtforward.
See https://www.nxp.com/docs/en/application-note/AN4948.pdf for more details.
What missing in AN, is the configuration of Debug Configuration to perform selected Target Task.
If you will go to Debugger tab and there Download tab, you may uncheck the "Standard Download" and select your own Target Task
RadekS_2-1698923710364.png
In such a case, the Flash Programmer will be executed directly by clicking on Debug button.
I hope it helps you.
BR
RadekS