Dark theme is in Early Access Program
The dark mode is still in EAP (Early Access Program) and your Jira Cloud instance needs to be part of the program to have it. Otherwise, the Issue Matrix app will still be visible with the default light mode preference. This will result in a “mixed” experience - Jira will be shown with the dark theme and the app with the light theme. You can find information on how to join the Early Access Program in Atlassian’s documentation.