In cases where the researcher publishes in a subscription journal that is covered by a Transformative Agreement, to which they have access, it is fully compliant with Plan S. As always, this is under the condition that the Plan S requirements for publication venues are fulfilled (see in Part II of the Guidance). To clarify: If a Transformative Agreement has been concluded between a publisher and a consortium of institutions, then, if a researcher at one of those institutions who is funded by a cOAlition S funder publishes an article in a journal that is included in the Transformative Agreement, this article would be compliant.
However, if another researcher supported by a cOAlition S funder, who is based elsewhere that is NOT covered by the Transformative Agreement, publishes in the same journal, then to comply with the Plan S requirements the researcher must make a copy of the article (either the Author Accepted Manuscript or the Version of Record) available in immediate OA via a repository (under a CC BY licence).