That approach might work if the prototyping is very simple, but I don’t recommend it. When the Edison module is programmed, the expansion board where it is connected to is considered when the muxes are configured. If you program the Edison using the Arduino Expansion Board, when you transfer the module to the Mini-Breakout Board you will probably get errors during execution because there are some muxes that are only available on the Arduino Expansion Board. Additionally, if you base your prototyping on the logic level of 5V used by the Arduino Expansion Board, then you will have to add a voltage level interface to the Mini-Breakout Board because its logic level is 1.8V.
Anyhow, if you are planning to use the Mini-Breakout Board at some point, then why don't solder all the pins and prepare the board for prototyping right away? That way you will be doing the prototyping using the Mini-Breakout Board and you will be sure that it'll work.