I have found another solution to the scenario 2 that I blogged about a couple of weeks ago (“The values in the output message are an aggregation of the two input messages with one value coming from only one input message“). This solution does not use custom XSLT just the BizTalk mapper.
I found if I used the Table looping functoid instead of the looping functoid I could get the correct transformed message as well.
[...] For a better solution see http://connectedpawns.wordpress.com/2009/03/08/many-to-one-mappings-using-the-table-looping-functoid... [...]
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