Whatever it might be executive-branch-wide if non-DOJ agencies were doing that, its a failure of leadership within DOJ if entities within DOJ are ignoring OLC opinions. Which is the issue here; the lowest common level of authority between FBI and OLC isn't the President of the United States.
Given that Congress constitutionally can, and does, assign functions directly to specific entities within the executive branch, the concept of the unitary executive, while not entirely lacking in validity, is limited even as a description of the Constitutional structure, much less practical and political reality.
> The OLC is like the executive's in-house legal counsel.
No, its not.
Its like outside (advisory but not trial, as the latter function is handled by, well, much of the rest of DoJ) counsel to executive branch entities other than DoJ, which all, in fact, also have their own in-house counsel.
To stretch the corporate analogy, it's like a large company that might have regional or divisional legal departments in addition to a general counsel's office. While the divisional departments may have specific roles and expertise, they cannot go their own way on matters of company-wide concern.
Comparing OLC to outside counsel ascribes to departments an autonomy they don't possess. A company is an independent entity with the prerogative to ignore its outside counsel. But agencies like the FBI are not independent. They're mere organizational units of the executive.