I found these while I was messing around with the development tools:
--joplin-font-family
--joplin-margin
--joplin-item-margin-top
--joplin-item-margin-bottom
--joplin-disabled-opacity
--joplin-button-min-width
--joplin-button-min-height
--joplin-editor-font-size
--joplin-text-area-line-height
--joplin-line-height
--joplin-header-button-h-padding
--joplin-toolbar-height
--joplin-toolbar-padding
--joplin-main-padding
--joplin-top-row-height
--joplin-editor-padding-left
--joplin-margin-right
--joplin-margin-left
--joplin-margin-top
--joplin-margin-bottom
--joplin-font-size
--joplin-toolbar-icon-size
--joplin-note-viewer-font-size
--joplin-background-color
--joplin-background-color-transparent
--joplin-odd-background-color
--joplin-color
--joplin-color-error
--joplin-color-warn
--joplin-color-faded
--joplin-color-bright
--joplin-divider-color
--joplin-selected-color
--joplin-url-color
--joplin-background-color2
--joplin-color2
--joplin-selected-color2
--joplin-color-error2
--joplin-background-color3
--joplin-background-color-hover3
--joplin-color3
--joplin-background-color4
--joplin-color4
--joplin-raised-background-color
--joplin-raised-color
--joplin-search-marker-background-color
--joplin-search-marker-color
--joplin-warning-background-color
--joplin-table-background-color
--joplin-code-background-color
--joplin-code-border-color
--joplin-code-color
--joplin-selected-divider-color
--joplin-color5
--joplin-background-color5
--joplin-background-color-hover5
--joplin-background-color-active5
--joplin-config-screen-padding
--joplin-color-hover
--joplin-background-hover
--joplin-highlighted-color
--joplin-cache-key