In order to do data cross referencing from one system to another, the Microsoft.BizTalk.CrossReferencing assembly could use an additional method with a signature like the following (plus the addition of a new accompanying cross reference functoids using this method)
public static string Convert(string sourceApplicationCode, string targetApplicationCode, string referenceDataTypeCode, string sourceSystemValue)
At the moment, you need to use two functions as shown in the code below:
string commonId = CrossReferencing.GetCommonID(referenceDataTypeCode, sourceApplicationCode, sourceSystemValue);
returnValue = CrossReferencing.GetAppID(referenceDataTypeCode, targetApplicationCode, commonId);
This implements two separate stored procedure calls. It would be easy to create a single stored procedure to do the job to make this more efficient, but then you would need to write custom data access code rather than using the provided assembly.