OK,I think I might know what you are talking about.
In the draft version (when you have the post open in your editor), the link is that tan colour with the light grey page background colour.
Then, the published version of the link (on the front-end of the website) is black, the same as the colour of the post text content.
The problem with the customizer in relation to the post editor is that whatever you change in the customizer for colours, it does not reflect in the editor because it applies your preview and the changes to the front-end of the site content, not in the editor.
I just tested the colour settings for the link colour and hover colour. I it worked for me on the front-end where I made my links green and the hover as red. But again, this change won’t show in the post editor; just how the customizer and WordPress works (at least right now).
By the way, is the front-end of your site posts using that darker tan colour behind the content?