We did a little more testing with Release 12 (MCU Version: 002.013). It looks like any call to pmtool shutdown (or a write to /sys/module/swimcu_pm/boot_source/enable will enable PSM and thus disallow ULPM. After the request has been made, it is possible to disable PSM through the AT command AT+CPSMS=0 at which point the device enters ULPM mode.
It is impossible to disable the PSM mode before hand because it seems that the ULPM shutdown request itself is what is enabling the PSM in the first place thus preventing the shutdown. So a theoretical way to have this work is to have the application software write to the sysfs file and then to send the AT command, not ideal but it could work.
I have not done any reliability testing on this solution.