The 68050 was planned to replace the 060 accelerator card to save money. The second advantage would have been that the 68050 would become faster with every new generation of FPGA. And it could be better integrated/combined with the chipset. On the other hand you need a bigger FPGA (that is the most expensive part of this kind of computer).
Gunnars project is some kind of spin off and would be different. As far as I understood the discussions it would be as fast as anyhow possible but not compatible with Natami.