If using automatic theme mode to switch themes when the OS theme changes (light/dark), it’s not currently possible to select custom themes for each mode.
This shipped in Mailspring 1.22.0 — you can now choose exactly which themes apply for light vs. dark when you’re in Automatic mode (Preferences → Appearance). Update via the in-app auto-updater or grab it from Mailspring - The best free email app. Thanks for the suggestion, and a shout-out to @Jayphen who implemented it!