What is a primarily confidential position? Who decides to classify said position? What is the nature of said position?

What is the meaning of "primarily confidential position"?

Prior to the passage of the x x x Civil Service Act of 1959 (R.A. No. 2260), there were two recognized instances when a position may be considered primarily confidential: 
Firstly, when the President, upon recommendation of the Commissioner of Civil Service, has declared the position to be primarily confidential; and,
 secondly in the absence of such declaration, when by the nature of the functions of the office there exists "close intimacy" between the appointee and appointing power which insures freedom of intercourse without embarrassment or freedom from misgivings of betrayals of personal trust or confidential matters of state

Every appointment implies confidence, but much more than ordinary confidence is reposed in the occupant of a position that is primarily confidential. The latter phrase denotes not only confidence in the aptitude of the appointee for the duties of the office but primarily close intimacy which insures freedom of [discussion, delegation and reporting] without embarrassment or freedom from misgivings of betrayals of personal trust or confidential matters of state

What are the examples of "primarily confidential" positions?

The following were declared in jurisprudence to be primarily confidential positions:
 Chief Legal Counsel of the Philippine National Bank;⁶⁰
 Confidential Agent of the Office of the Auditor, GSIS;⁶¹
 Secretary of the Sangguniang Bayan;⁶² 
Secretary to the City Mayor;⁶³
 Senior Security and Security Guard in the Office of the Vice Mayor;⁶⁴ 
Secretary to the Board of a government corporation;⁶⁵ 
City Legal Counsel, 
City Legal Officer or City Attorney;⁶⁶ 
Provincial Attorney;⁶⁷ 
Private Secretary;⁶⁸ and 
Board Secretary II of the Philippine State College of Aeronautics.⁶⁹

Cite some examples of positions which are not considered as primarily confidential?
Consequently, brought upon by their remoteness to the position of the appointing authority, the following were declared by the Court to be not primarily confidential positions:
 City Engineer;⁵⁰
 Assistant Secretary to the Mayor;⁵¹
 members of the Customs Police Force or Port Patrol;⁵² 
Special Assistant of the Governor of the Central Bank, Export Department;⁵³ 
Senior Executive Assistant,
Clerk I and 
Supervising Clerk I and
 Stenographer in the Office of the President;⁵⁴
 Management and Audit Analyst I of the Finance Ministry Intelligence Bureau;⁵⁵ 
Provincial Administrator;⁵⁶
 Internal Security Staff of the Philippine Amusement and Gaming Corporation (PAGCOR);⁵⁷ 
Casino Operations Manager;⁵⁸
 and Slot Machine Attendant.⁵⁹ All positions were declared to be not primarily confidential despite having been previously declared such either by their respective appointing authorities or the legislature.