It looks like MsfinderConsoleApp attempts to open reference data in a read/write mode, which makes it impossible to install them in a shared location on an HPC cluster. Here is the system call
open("/apps/ms-finder/3.5.0/Resources/NeutralLossDB_vs2.ndb", O_RDWR|O_CLOEXEC) = -1 EACCES (Permission denied)
MS-FINDER is also looking for LipidQueries.INI in the installation directory and fails to being a run when it's not present, but that file is not in the distribution and is not described in the tutorial.
It would be great if none of the console programs in MS-DIAL/MS-FINDER required write access to their installation directories. Usually, any files that need to be written to must be in the user's current working directory or command-line arguments should be made available to allow users to specify their locations.