A theme is exactly that. A pre-set color-scheme.

Even when switching between dark/light system settings, chrome just internally switches between its dark and light themes unless the user has specified which they prefer. See Browse in Dark mode or Dark theme for further details on that, but at the moment which theme to use is selectable at the bottom right of the New Tab page.

Presumably, if a user likes your theme, they'll pick it regardless of their OS setting just like if they selected manually from one of Chromes built-in themes. If you want to provide choice, upload two themes: one light and one dark. The user then makes the choice when they install your theme rather than care about the OS setting.