As a workaround, the customer can use the GUID value of ims.0000-ID-Source-All-0000 to state that this is referring to all identity sources in the system.
As an example, when connecting to the WSDL of the RSA Authentication Manager:
$SystemFilter = New-Object mjb.Filter
$SystemFilter.comp = New-Object mjb.Empty
$SearchPrincipalsCommand = New-Object mjb.SearchPrincipalsCommand
$SearchPrincipalsCommand.limit = 100
$SearchPrincipalsCommand.identitySourceGuid = 'ims.0000-ID-Source-All-0000'
$SearchPrincipalsCommand.securityDomainGuid = 'ims.000000000000000000001000e0011000'
$SearchPrincipalsCommand.systemFilter = $SystemFilter
$SearchPrincipalsCommand.searchSubDomains = $true
$SearchPrincipalsCommand = $CommandServer.executeCommand($loginCommand.sessionId, $SearchPrincipalsCommand)