I don't understand your problem, in fact, are you having a problem or you just think there is a problem?
The purpose is to avoid the huge amount of source-target DTL processes while working with several hundreds of Rules
First, rules do not modify messages, only DTL may modify a message.
Did you measured and verified this supposed "huge amount" or you think/guess this is actually happening?
Please note that HL7 storage is complex/advanced and very efficient, only changed segments are actually duplicated in storage, even from different HL7 messages.
Did you actually checked what is actually stored in your scenario?
I feel and believe that you are looking for a solution to a non existent problem.
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