tl:dr – use sudo to launch sublime before changing settings (or they won’t persist).

In addition to using sudo, you need to edit the font preferences in the user’s preferences as opposed to default preferences (apparently the platform prefereces override the setting, and are between default and user in the heirarchy, but not listed in the menu for some reason).

I copied the font size property from the general preferences, and pasted it into the user prefs, which looks something like:

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{
    "font_size": 14
}

Feel free to comment if I’ve misunderstood this :)

PS – the same seems to be true of entering your license key – make sure you start sublime using sudo, or it wont persist.