We'll see how this ends up, I can't really judge what is going on with government agencies in this country.
The only personal observation I have is that apparently the DFA has a significantly higher budget to spend for their premises in Dumaguete (upper level in Robinson's, plenty security guards, nice looking office) than the BI (cramped office in third rate location, furniture that outlived its usefulness).
To me that seems like a truly silly difference.

As for the conflict regarding express lane fees / overtime pay I only have the media reports to go by.
From the reporting it would seem that it is a combination of underpaid staff (regular wages) and a long standing (bad) practice to augment salaries with exorbitant overtime pay.
In an ideal world this would never even have been considered as a "solution", and instead the BI's wage structure/levels should have been examined and fixed long ago, but in the Philippines one can't expect things to work that way I guess.

I do assume that the president of the republic has not acted on an impulse when deciding the 3 billion or so in express lane fees henceforth need to be deposited in the government coffers instead of being used for paying overtime at the BI though. Thus an exodus of unhappy personnel cannot come as a surprise.
I would expect the BI to hire new (extra) staff in a hurry, but unless the Dumaguete office is abandoned for a larger one I can't imagine any extra staff being assigned there lol.

 

And yet they can not provide a certified photocopy of my wife's passport - a passport she got at that office. CrAzY

 

Perhaps if they had more integrity, government workers wouldn't be so despised. Drain the swamp.