Managed to solve it, I just needed to pay more attention to the docs.
Synapse has 2 type of api:
- classic azure management rest api
- data-plane rest pi
synapse internal object management is done through data plane api, so things like pipelines, activities, triggers, notebooks etc are in the scope of data plane api and to use them with Managed Identity auth you just have to specify the correct Resource in order for the token issuer to include the right scope. So for Data Plane api you would wanna use
"https://dev.azuresynapse.net/" as resource, opposing to the classic "https://management.core.windows.net/".
see also here:
https://dev.to/jayendran/azure-synapse-analytics-workspaces-deploy-and-debug-part-2-l5c
https://learn.microsoft.com/en-us/rest/api/synapse/#common-parameters-and-headers