There is already a bunch of documentation on cmdlets, let’s do a slightly deeper dive than the cmdlet documentation provides.
The values that you provide to Outlook Anywhere settings can be classified into 2 types of properties – client facing and server facing. Examples of client facing properties are ClientAuthenticationMethod, External Host Name. Examples of Server facing properties are IISAuthenticationMethods, SSLOffloading. Client facing properties are picked up by Autodiscover and supplied to Outlook to configure client access to the Outlook Anywhere service. Server facing properties are picked up by a servicelet called RpcHttpConfigurator which runs as part of the Microsoft Exchange Service Host service. This servicelet runs every 15 mins by default, but the interval can be adjusted by changing the value of the HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\MSExchangeServiceHost\RpcHttpConfigurator\PeriodicPollingMinutes regkey. Note that setting this value to 0 turns off the RpcHttpConfigurator.
When the RpcHttpConfigurator runs, it picks up the IISAuthenticationMethods and SSLOffloading values from the AD and stamps it on the \rpc vdir settings in the IIS metabase – overwriting any previously set value. This means that if you manually change the settings on this vdir, you should expect to be run over pretty shortly by the RpcHttpConfigurator (unless you have set the reg key to 0).