lol! i used to visit my PO so often that now they just send me an SMS whenever i have more than 4 boxes or at least one of them is a month old, whichever comes first. you're spot on with the tax calculations.
NY price for SV-51 + 3k yen shipping works out to around 17k Php shipped. Add ~4k Php for taxes and the 112 Php fixed postal handling fee, for a total of 21k php. there's a local PO for the SV-51 at 22k Php, less 10% if a member, so net 20k Php.
as of late 2016, any importation less than 10k Php item value only (ie. excluding shipping) is exempt from taxes. hence i have since split my shipments into smaller chunks. and high value items ship individually. when i have a big order at NY (eg. to maximize a discount coupon), i then select the ship separate parcels option which only costs a little more.
BOC occasionally makes errors by computing based on landed cost even if the item value alone is under 10k. i just point out the error to the local PO and they release the package tax free.
this is really odd. sorry man, but it really looks like you were over taxed.
i paid 3k Php tax for the same item, and my shipments from Amiami, HLJ, HS always had the shipping cost spelled out. in Amiami's case, it's not on the invoice but on the declaration sheet under "postage charges". both pieces of paper are inside a plastic bag pasted on the box.