Hello @Sam Hodgkinson
Thank you for reaching out. I would like to confirm that you can create Azure AD SAML applications using PowerShell or Graph, however SAML Claim management/transformation currently can only be performed from Azure AD Portal.
I assume we do not have an option to edit SSO Claims or setup SAML Claim transformations using Microsoft Graph or Azure AD PowerShell.
I hope this helps and hence would request you to please "Accept the answer" if the information helped you. This will help us and others in the community as well.