I believe, at least in Jakarta, the 5% transfer taxes (SSP for the buyer) are computed as a function of the NJOP value. Seems logical because to do otherwise would open the process to massive and constant abuse, just of the sort suggested by your buyer. Sounds to me like it might simply be a ploy to get you to pay the buyer's tax or at least part of it. Keep in mind that there is no sanctity of contract here; the price is subject to negotiations up until the money changes hands, regardless of what's in writing.
Notary fees and commissions, if any, are also subject to negotiation. There are some rules of thumb, but they are often completely ignored in the process of negotiating terms. If the buyer, or you for that matter, think the notary fees is excessive then ask for a lower price and be prepared to walk if you are not satisfied. Notaries are like Angkat, they are everywhere and unscrupulous for the most part.