Interesting article, but no mention of pandemic quarantines or isolation.
Precedent for local control goes back quite aways (1918 flu pandemic):
https://blog.history.in.gov/tag/pandemic/
That is not a complete listing of presidential powers during a National Emergency, and I have no doubt at all that Trump and his team working on this will not allow states to keep in lockdown, and know the exact ways and means to stop it.