Actually the real answer may not be a simple yes or no
Technically, all Filipino's granted 'immigrant-class visa', (includes work permit visa's) are required by the Philippine Government (Article 19 of Presidential Decree No. 442) to register with the CFO and attend the Pre-departure Orientation Seminar (PDOS) before leaving.
If he's been properly registered he will have his CFO sticker.
This is supposed to be inspected by the BI at departure.
Unless you can see what visa is actually in his passport there's really no way to know anything 100%
But look, from what you've said it certainly appears that he may well have attempted to leave with an immigrant-class visa but without his CFO sticker and that's why he was refused exit on 5 July.
