Most notaries will provide a line item spreadsheet, prior to closing, itemizing each cost. You cannot avoid these closing costs as a buyer. They are an obligatory part of the legal process that allows a buyer to safely obtain property in Mexico.
The largest fees are the transfer tax, notary fees and the appraisal. These fees are all based on the appraised tax value, not the actual purchase price. In general, the appraised value is about half of the purchase price. When the appraised value comes in high, the overall percentage paid at closing will increase. The appraised value often comes in quite close to the tax value you see on your annual predial (tax bill). By law, it cannot be less than that.
Occasionally the Notario will negotiate their fee. They do not have to. Some Notarios charge more than others and in some cases even actually provide MORE or BETTER service and accuracy in exchange for the higher fees. What a concept.