As long as your header has been provisioned in a mailbox https://learn.microsoft.com/en-us/exchange/client-developer/exchange-web-services/how-to-provision-x-headers-by-using-ews-in-exchange (eg a least is been used once before) you should be able to use SingleValueExtendedProperties to do that but not in the initial createReply request eg this is what works for me
{
"SingleValueExtendedProperties": [
{
"Id": "String {00020386-0000-0000-C000-000000000046} Name x-my-custom-header",
"Value": "Some Value"
}
]
}
then you patch the draft message with your extended property for the x-header
and then Send and your x-header should get added