You could try using the productVariantCreate mutation instead to see if this works with GraphQL. You could try with the GraphiQL tool and the mutation would look something like:
When I tried to run it and to add a new variant to product with linked option I got an error
Internal error. Looks like something went wrong on our end.
Request ID: e06ddcce-4f9b-45fa-9483-2e1709e84759-1722438715 (include this in support requests).
When I change product ID and tried to insert it to product without linked option it worked without an error.