internal rules set by employer is part of management prerogative. if employee does not agree with the rules, they are free to get out or look for another job. but in some cases, you can question this to NLRC.
as long as your are paid with your work, whether it's daily, weekly, monthly or even hourly, it's legal. what the law prohibit is involuntary servitude where a worker is not paid for his service rendered.
DOLE ruling is not confusing. the presumption is, employer should pay its worker, regardless if it's monthly or daily basis.
In all cases, feel free to read Labor Code Chapter III and IV, pag may mga articles dun na sa tingin mo ay na-violate, you can go to NLRC to file a labor case.
Art. 102. Forms of payment. No employer shall pay the wages of an employee by means of promissory notes, vouchers, coupons, tokens, tickets, chits, or any object other than legal tender, even when expressly requested by the employee.
Payment of wages by check or money order shall be allowed when such manner of payment is customary on the date of effectivity of this Code, or is necessary because of special circumstances as specified in appropriate regulations to be issued by the Secretary of Labor and Employment or as stipulated in a collective bargaining agreement.
Art. 103. Time of payment. Wages shall be paid at least once every two (2) weeks or twice a month at intervals not exceeding sixteen (16) days. If on account of force majeure or circumstances beyond the employer’s control, payment of wages on or within the time herein provided cannot be made, the employer shall pay the wages immediately after such force majeure or circumstances have ceased. No employer shall make payment with less frequency than once a month.
The payment of wages of employees engaged to perform a task which cannot be completed in two (2) weeks shall be subject to the following conditions, in the absence of a collective bargaining agreement or arbitration award:
1. That payments are made at intervals not exceeding sixteen (16) days, in proportion to the amount of work completed;
2. That final settlement is made upon completion of the work.