I’ve looked through the appearance menu, but was unable to find the option. I’m trying to change the default yellow to another, less-obtrusive, color for my eyes
Firstly, footnotes are not yellow by default! You are using, it sounds like, linked comments instead. They appear in a sidebar, I’m assuming, and are yellow as well as the box in the editor that they are linked to? Right-click on those in the Inspector and select “Convert to Footnote”. You can do that to bunches of them at once by selecting them all in the sidebar.
Footnotes are always all the same colour, and by default they are grey. If this is still too heavy on the eyes, you can change the global default in the Appearance preference pane. Setting it to white will effectively make it appear transparent in the editor (if it is white, of course, as well).
The option you are looking for is in the Editor section of “Customize Colors”, under “Footnote Comments BG”.
You’re correct. I meant to write linked comments.