In my experience doing weird things with mountpoints, there is almost always some bug that happens on reboot of the system. For example, if your mounts aren't in /etc/fstab, they simply won't be restored. And if you have a script that sets them up manually, then make sure that script runs on boot after any mounts it implicitly depends on.

Also note that any scripts with config stored in these mountpoints (which seems to be the point of the tool) will not be able to run until the mountpoints are up. That seems like an obvious observation, but it's easy to fall into a trap where one of your scripts installed with this tool is called in a setup script that runs on boot of your machine.