Directing the outcome is different because Congress prescribed an objective standard for tax exemption, which is clearly within its legislative power; the President can't override that any more than he can unilaterally increase or decrease the amount of tax due.
At least, that seems to be the implication of the unitary executive theory. And even if that is beyond existing precedent, Seila Law suggests that the President could call the Commissioner of Internal Revenue, express his desire to see such an investigation, and then fire him/her for not doing so.