$1600 is a bit high as a replacement cost when you were already spec'd out the Fusion system. But the fusion system is only like $300 anyway. The increase is not too bad considering you are moving to one of the best salt systems on the market.
Make sure to be clear with him that you do not want the mineral cartridge added to the vessel. In fact, as soon as it is delivered, grab the starter cartridge out of the box and put it away. If he gives you a free cartridge grab that one as well. My builder gave me a regular cartridge and the unit also comes with a starter cartridge (doesn't last as long as the regular one). You can sell both these on ebay for like $200.
I guess the confusing part is that we are at $60K speced w/ IFCS and Natures2. When i swap out Nature2 SOFT SWG and remove IFCS we are at $63K....can't understand the math...