Did you ever find a solution for this? I found the cause of this but the code is really not easy to follow so it is unclear to me how to fix the issue.
What is happening is that because IgnoreDefaultSfo is true (by way of using GenerateSFO=true) it excludes the param.sfo that would normally go in the root of sce_sys in the disc layout in favor of the title specific param.sfo. The problem though is that then it maps that param.sfo to sce_sys/[title_id]/param.sfo. The Sony packaging tool seems to demand it be in the root of sce_sys/ and errors.
If you change the targ_path value for it in the gp4 to sce_sys/param.sfo and run the sony packaging tool with the same params as buildcookrun used, it will actually make the package.
The problem for me is even knowing what is going on I am unsure of how to proceed to make it work. Should I just hack something into the PS4 automation code that always maps param to sce_sys root or is there something else I should be doing?