I’m using a “dark mode” theme and when I “footnote” a selected area (one which I usually already have highlighted) Scrivener adds an additional highlight over the text; one that matches the dark-theme seen in the inspector. Is there a way in which I can turn off the text highlighting (only) in the main editor?
This above would hide the highlight pertaining to the footnote of editor text.
. . . . . . . . . .
This below would allow you to rather set it to a different color.
[Edit] I just saw from your profile that you are actually running Scrivener V1… (?) These are instructions for V3.
You should make sure to mention it (that you are running V1) when posting. Or fix your profile if you are rather running V3. Or upgrade. 
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Sorry about the Version omission, but I am running the newest version now. BTW…I tried changing the “hide markup” box before I made this post…and I didn’t see any change? Also, when you change the “footnote background” it also messes up the background in the inspector.
Hide markup is a two parts thing.
1- the hide what (set in the options)
2- hide or show
See both my first two screenshots.
Yes
Pick a color that won’t make you want to describe it as “messed up”.
Ah ha!..that first pic was what I was missing! Thank you very much!
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A bit off-topic as it relates to Comments, not Footnotes…
I have a problem with Hide/Show Markups in Comments. (Alt+Shift+H)
I’ve ticked the box for Comments in File > Options > Appearance > Textual Marks > Options Tab … “Hide Markup hides”. (That gives the ability to hide and show.)
Then, when I comment on text, the default is to show the markup (background colour of text in the same colour as the background of the comment). Alt+Shift+H switches it off. Happiness.
However, if I exit Scrivener and come back in, the markup colour is part of the text again.
I then need to select Alt+Shift+H twice to switch it off again, but an app restart brings the markup background back.
Is this normal, expected behaviour? I tested it on the Interactive Tutorial and get the same result. See here:
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Sentence in yellow is the background markup colour of the comment.
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Alt+Shift+H has switched it off.
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Exited the project and returned to the project–and the coloured markup background is back.
My second query is, does it only work per document?
I ask because in my WIP I switch off one document and it seems to randomly appear in other documents.
Since I work with different colours for backstory, foreshadow, red herring and (simple) comments, and already control the first three with font colour changes, my WIP is becoming a psychedelic nightmare, albeit a pastel coloured one, and I’d like to hide all of Comments’ markup background colours permanently in Scrivener’s editor… but it’s not happening.
I’d say the feature is buggy.
Yes, I would say it is a bug.
But… I just tested it and can’t reproduce. Hide Markup sticks after a close / restart.
Else, you could at least set the comments to your editor’s background color, so they won’t be that annoying to you. (They will still have a tiny box around them, but it is not as eye catching as the highlight.)
Thanks. I’ll test again over the weekend and raise a bug if the problem persists.
I may have some third-party add-in interfering with things.