You can change the Server name in the database by performing this query:
Update [MSCRM_CONFIG].[dbo].[DeploymentProperties]
Set NVarCharColumn = 'dynamics.company.com:80'
WHERE
ColumnName in (
'ADDeploymentSdkRootDomain',
'ADDiscoveryRootDomain',
'ADSdkRootDomain',
'ADWebApplicationRootDomain')
I used this in a test environment where the URLs listed on the Developer Resources didn't include the Domain name, and needed to.