It really was terrible. The audio transcription puts you right there and just wow.
Like you said think it was a number of factors, but I think the other ones only compounded the situation after the master committed the ship to the float plan. He looked at an outdated weather report, didn't know the software options to plot the up-to-date hurricane overlay, company didn't permit any of the crew to have access to the ship's satellite phone (and presumably internet access that came with it) for a double check, then he dismissed a confrontation about the conflicting NWS report from the 2nd mate, then delayed pulling up updated information from his lagging weather report and went to sleep.
The design of the ship played a factor too. It was a retrofitted RO/RO ship with waived safeties, and had ventilation hatches that apparently lowered the de-facto lowest-point-of-water-ingress (forgot the actual parameter name) underneath the unsecured hatches, which were - unsecured. Or unreliable. New engineer started doing maintenance mid-storm, lowering the engine's power output, and I think the loose cargo became a factor afterwards.