Goodness me you're right!...the standard photo's from a booth for passports are the right size, so I will use that. What threw me is the reacquisition form shows 2 boxes for photos (with the dimensions marked in them 4.5 times 3.5) but the boxes are actually square (4.5 x 4.5).
I forgot all about biometrics so obviously they already have the passport photos presumably. However, one does wonder, having read others comments, what the point is in actually getting a Philippines passport if you don't need it to enter the country!
Thanks everyone for your responses.