This post has some time now, but my answer might still help someone.
So you have to bind the Trusted Certificate policy on your payload.
E.G.:
Imagine that you have a Trusted root certificate with Policy ID '123456ab-1234-56df-97ce-12ab34cd5678'
The property would look something like this:
rootCertificate@odata.bind: "https://graph.microsoft.com/beta/deviceManagement/deviceConfigurations('123456ab-1234-56df-97ce-12ab34cd5678')"
The Payload example to create a Windows8.1 Scep profile would be like this:
{"id":"00000000-0000-0000-0000-000000000000",
"displayName":"W81SCep",
"description":"",
"roleScopeTagIds":[],
"@odata.type":"#microsoft.graph.windows81SCEPCertificateProfile",
"renewalThresholdPercentage":20,
"subjectNameFormatString":null,
"certificateStore":"user",
"certificateValidityPeriodScale":"years",
"certificateValidityPeriodValue":1,
"rootCertificate@odata.bind":"https://graph.microsoft.com/beta/deviceManagement/deviceConfigurations('123456ab-1234-56df-97ce-12ab34cd5678')",
"subjectNameFormat":"commonName",
"subjectAlternativeNameType":"userPrincipalName",
"keyStorageProvider":"useSoftwareKsp",
"keyUsage":"digitalSignature,keyEncipherment",
"keySize":"size2048",
"hashAlgorithm":"sha2",
"extendedKeyUsages":[{"name":"Any Purpose","objectIdentifier":"2.5.29.37.0"}],
"scepServerUrls":["URLSCEP.com"]}
This 'rootCertficate' property can be found in the main API reference page for Windows8.1Scep profile as a "Relationship" property. You can find it here:
https://learn.microsoft.com/en-us/graph/api/resources/intune-deviceconfig-windows81scepcertificateprofile?view=graph-rest-beta
It's really not very straight forward, I had to inspect a request on the Azure Portal to find out.