I agree. It ought to be system default. If you like the dark theme, you would set it as your system default. If you don't, you would keep the light theme as your system default. Why change it in multiple places?
(While I'm at it, I have the same annoyance for many other things too that disrespect consistency, for example the font sizes on
medium.com - if I wanted large fonts I would change them in my browser settings for all sites.)