If you have to prototype something like that, it is probably better to use adaptor PCBs, and break out the pins to 0.1" connectors. When designing a PCB for a prototype, the trick is not to get too "clever" with packing tracks together or fully minimising RFI emissions. It is very tempting to show something approaching a final product, but mistakes do happen, and it is better to have PCB tracks that are visible and that you can hack around a bit.