The easiest change that Discourse could make now to increase the likelihood that summary emails are displayed correctly in dark mode would be to not enable the apply custom styles to digest site setting by default. (Note, this will only affect iOS email clients.)
Another small change would be to update the copy of the digest logo site setting to encourage uploading a logo that has sufficient contrast when displayed against either a light or a dark background color. The go-to trick for dark logos is to add a white outline to the logo.
Possibly, the Emails / Preview summary page should give a warning that some email clients will perform a “full color invert” when the email is viewed in dark mode. Site owners could be encouraged to test their summary emails in dark mode on whatever email clients they have access to.