After a lot of trying I managed to finally get a prestage package installed, after checking the hash and the size more carefully.
I still have an issue while trying updating the package:
I changed the script inside the package, and uploaded it to Jamf Pro.
I set up the computer with the same prestage setting, and as I checked, the correct package was installed.
What happens next is weird - after a few seconds, the old version returns, instead of the new one!
I can see it change live if I open the folder that the script is in during setup assistant also.
Does anyone knows about this issue, and how to resolve it?