Sorry for the break, had to get on with some other work...
Just like ScriptExecutionTimeOut I can change other values, providing I add 'SiteSettingsKey=x' to the query, eg
Set-WmiInstance -Path "root\ccm\policy\machine\actualconfig:CCM_ConfigurationManagementClientConfig" -Arguments @{SiteSettingsKey=1; ScriptExecutionTimeOut=400}
Set-WmiInstance -Path "root\ccm\policy\machine\actualconfig:CCM_ConfigurationManagementClientConfig" -Arguments @{SiteSettingsKey=2; PerProviderTimeOut=300}
The above both 'work' and don't give an error but if I run up a WBEMTest session in that namespace/class, SiteSettingsKey always equals NULL. From what I can see there doesn't appear to be a way to fix this problem on a client in provisioning mode. Open to any other ideas though!
BTW when SiteSettingsKey = NULL you are unable to query the class (but you are able to enumerate it in WBEMTEST). You can only query the class if the value is 1 from what I can see.