During website creation on the Configure Service step not all account's domains are listed.
Why does it happen?
The domain will not be listed if it has A, AAAA, CNAME or MX records.
This behaviour will be improved in scope of requests WHM-10196 and PRF-70, in a way to allow usage of a domain in WebHosting Linux alongside with other services like Office 365 or Exchange.
Please, contact your Technical Account Manager to trace status of requests.