It's a good idea to consider WITH_TRA whenever you have more than a single TRA file. Generally, WITH_TRA obsoletes USING (and to a some degree also LOAD_TRA). Additionally, since WITH_TRA has local scoping and can be nested, you do not necessarily need to worry about keeping your different TRA files free of overlap (e.g., you can start all your TRA files at 0).
As an example, I have this code in aTweaks:
COPY_EXISTING baldur.bcs override
DECOMPILE_AND_PATCH BEGIN
REPLACE_TEXTUALLY ~\(SetGlobal("drowEraseJournal","GLOBAL",2)\)~ ~EraseJournalEntry(@58) EraseJournalEntry(@59) \1~
END
BUT_ONLY
@58 and@59 are pulled from a component-specific TRA file. Before, you needed to have them in setup.tra (e.g., QuestPack had a lot of this) and somehow cope with the associated difficulties (say, the need to have different text encoded in different charsets), or you have to do like me and use a very ugly hack involving LOAD_TRA. Now, you can just wrap the action in WITH_TRA and neatly solve the problem that way.