Как я должен изменить цвет подсветки по умолчанию на цвет, который я хочу?

к сожалению, нет никакого способа изменить цвет по умолчанию, желтый на другой согласно этой ссылке https://help.gnome.org/users/evince/stable/annotation-properties.html.en

Customize annotations

    In the Annotation Properties window, you can change the author, color, style and icon of your note.

    The annotation properties will be applied to the note for which you made the changes only. Each note can have a different set of properties.

Can I permanently change the default annotation properties?

The default annotation properties (author, colour, style and icon) can only be changed on a particular note as stated above. So if you want all icons for your notes to be red instead of yellow, you will have to change the default from yellow to red individually on each note. There is no way to save different default settings for annotation properties, at this time.