As far as I can tell not only does the new Mastodon ToS apply to activity pub flows, it also heavily restricts the kinds of activity pub flows permitted by Mastodon instances that adopt the ToS, and also restricts what can be done with the results of those flows; while also claiming disproportionate rights to any content submitted to the service (i.e. we can use your content, you can't use ours).
Unless the ToS is more tightly scoped, this has very broad implications for the fediverse at large.