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I was able to run the following commands on my local HS 2018 %SYS namespace to create an application:

Set tWebAppName = "/csp/healthshare/samples/myapp"
Set tProperties("NameSpace") = "samples"
Set tProperties("CookiePath") = "/csp/healthshare/samples/myapp/"
Set tProperties("MatchRoles") = "%DB_CACHE:%All"
Set tSC = ##class(Security.Applications).Create(tWebAppName, .tProperties)

The above code works to assign the MatchRoles, but don't know if that answers your question.  I'd suggest running the delete command between attempts via: Set tSC = ##class(Security.Applications).Delete(tWebAppName) until you programmatically get exactly what you are looking to create.

You need to have the inbound message sent to this function.  Let's call it pRequest

#dim tMshSeg As EnsLib.HL7.Segment
#dim tPidSeg As EnsLib.HL7.Segment
Set tNewMsg = ##class(EnsLib.HL7.Message).%New()
Set tNewMsg.DocType = "2.3.1:DFT_P03"
Set tMshSeg = pRequest.getSegmentByPath("MSH", .tStatus) $$$ThrowOnError(tStatus)
Set tPidSeg = pRequest.getSegmentByPath("PID", .tStatus) $$$ThrowOnError(tStatus)
Set tStatus = tNewMsg.setSegmentByPath(tMshSeg, "MSH") $$$ThrowOnError(tStatus)
Set tStatus = tNewMsg.setSegmentByPath(tPidSeg, "PID") $$$ThrowOnError(tStatus)
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