The User Files preference is the default for all User Files. It affects your primary font when making a new note, making a new user tool, and possibly a couple other defaults. Changing it won't affect any existing notes, it is just the default for new items.
The User Note Display is the actual display for your specific notes file. As with all of our other Set ___ Display preferences, the changes only apply to the open tab or pane, unless you click 'Use as Default', which then would have it apply to any future instances of that Notes File.
Normally, the Set Notes Display lets you choose things not related to editing of the note, such as the Leading/Line Spacing, the Background Color, Search Highlighting, etc. The reason the font choice is dimmed without standardizing is because the font is normally chosen while editing a note. If the user actually wants to change the font used throughout the entire note, that is the point of a Standardization. If standardization is off, then whichever font, size, and style used when editing the note will be respected.
However, if I were you, I wouldn't be afraid of using a standardization from a Greek or Hebrew perspective. The code will still render Greek and Hebrew properly, using their chosen fonts in Preferences -> Unicode Display. You only want to avoid standardizing if you have varying sizes and styles that you wish to maintain.