Was looking for pretty much the exact same thing, this doesn't seem to be possible with normally exposed objects as you point out, but VBA macro + Outlook Redemption allows conversation topic to be tweaked easily. Bonus, the original message subject is unchanged, but the messages still show in a nice neat conversation group.
Something like this, thrown into VBA Macro and then run this script as a Rule action when messages are received with whatever criteria you determine:
Sub MsgProcess(msg As MailItem)
Dim oNS As Object
Dim oRDOSess As Object
Dim oRDOItem As Object
Dim sEntryID As String
Dim sStoreID As String
Dim NewConversationTopic As String
Set oRDOSess = CreateObject("Redemption.RDOSession")
Set oNS = Nothing
Set oNS = Outlook.GetNamespace("MAPI")
oNS.Logon
oRDOSess.MAPIOBJECT = oNS.MAPIOBJECT
sEntryID = msg.EntryID
sStoreID = msg.Parent.StoreID
Set oRDOItem = oRDOSess.GetMessageFromID(sEntryID, sStoreID)
'Apply what modifications to topic you want here - dumb example string manipulation shown
NewConversationTopic = Replace(oRDOItem.ConversationTopic, "BLACK", "WHITE")
oRDOItem.ConversationTopic = NewConversationTopic
oRDOItem.Save
End Sub
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