Plugboards have no effect on metadata being used to make collections, with the exception of title_sort and author_sort.
Put the tags you do not wish made into collections inside [ ] characters, as in [TODO.xxx.yyy].
You can also do it as you described, using a composite custom column 'built from other columns, behaves like tags'. I imagine that you would want to hide this column on the library view and not check the 'show in tag browser' box.
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