If you have a 64-bit ALU, you can change the microcode to make the instruction format whatever you want.
There is a lot more to a CPU than a simple ALU. There are lots of special registers, tables, control lines, etc. that need to be changed to support a 64-bit architecture, and especially a hybrid that can support many modes. Now there are some things you can do in microcode to make your processor look more like another architecture, but performance is going to be terrible if you don't have some optimized hardware to back it up. Addressing and mode changes are not isolated to just microcode changes.