I am a student so take this with a big pinch of salt!
If I wanted to do a System Usability Test as a new employee, I would firstly learn about the company’s users to identify clear users “personas” or categories - such as sales team vs human resources team vs engineering team vs warehouse team, etc. As you said different users / stakeholders have different needs from the system. Once you know to whom does the System has to serve and how, then I would prepare the SUS accordingly by user category and by priority, most common user persona group to lesser common. Then SUS the top priority categories, maybe discuss your finding at this point with your boss for their opinion of what outcomes would be most interested for the company for you to research further. This would make it even more relevant to your company, as you are new you cant know all. Don’t forget to check if your company’s System is used also by third parties, such as suppliers or delivery people, for example. As these would also be users with needs and you may identify very valuable data.
best of luck!