Sorry, let me try to spell it out one more time.
The constitutional position is as you say: Whitty is an advisor to government, he advises on policy, they decide.
The practical position at the moment is that government are failing to make the decisions necessary to protect the public, so Whitty finds himself issuing advice directly to the public that goes beyond the extent government advice, and to that extent, he is in practice setting policy.
Tory MPs are right that this is unconstitutional.
I say thank God for someone like Whitty.