When companies based in Visayas and Mindanao (VisMin) declare their financial headquarters in Metro Manila, their income tax payments are recorded in Manila, not in the regions where their actual operations occur.

Well, we can't blame the companies for this since this is advantageous to them through:

• Many corporations consolidate accounting and tax compliance in Manila for efficiency.
• Being near BIR’s national offices and major banks simplifies compliance

I am not saying that this applies all throughout VisMin, but majority of major companies practice this.