Is this something to do with the fact that I’m the msp? And under ‘Show More’ > ‘Azure’ it shows my tenant linked, although it shows the wrong onmicrosoft domain?
Do you mean that when you open the deployment, there are no computers listed on the right for you to click “Deploy” on? I think that is expected for Metascript filters as they need to do extra work (eg check if the primary user has a license).
Maintenance will still pick up the deployment as expected.
What James says about metascript filters is correct.
The metascript filter needs to execute against the computer to run.
You can also check the view logs button on a session and see the resolution of the 365 deployments using the metascript to see if they have returned true/false/or even a message about needing to configure the Azure integration for that tenant