It is kept separate as it is not tied to the theme, view, images, files, or templates in any way. The add-on may not always need updating when the theme does, as themes typically need updating for every update XenForo software does.
Install/upgrade TH themes from XenForo ACP
Extend permissions and user preferences for stylistic features
Uncollapse sticky threads on new reply with various options to control this
Iconator icon list stored for using icons such as FontAwesome all over XenForo
Social media, footer, common content stored across all themes in one place
Node grid and node CSS/class/icon management