So I followed the advice of the below answer to attempt to remote into my Mac mini from Ubuntu 16.04 with VNC Viewer. Everything is working fine except for Command key combos.
While attempting to troubleshoot, I opened the keyboard viewer, which is showing me that Command keys are being detected when pressed alone, but when pressed in combination with other keys, the last key pressed overrides it. According to the keyboard viewer, other key combinations do work as well.
I am open to using a different VNC program, but I don't know which if any will fix this problem.
UPDATE: It works in full screen, but not otherwise