Vincenze I don't really get what you're saying. The mini breakout isn't really designed for shields. If you're using one it would make more sense for you to go with the Arduino board or a custom pcb in general. They come that way because it is how you want it for most projects and very few people will ever solder/ desolder anything on the mini breakout board. What kind of shield are you using (just out of curiosity)?
Can you explain how to utilize the pin GPIO45, for example, on the breakout board without soldering a header?
I can create a custom pcb that has no power and FTDI chips and connect it to the breakout board like in the world of Arduino.
Sparkfun sells a few shileds. So, you can get the idea.
Ok, explain how you can connect an audio Digital-to-Analog Converter with the Arduino board.
I did this (pictured) an idea I got on this board - sorry I can't credit the author but it is brilliant - brining out most of the important GPIO's - uses simple point to point wires and headers.
Frankly, as you suggest, I have gone with the full line of sparkfun boards - they do all of the level translations (1.8v > 3.3-5v) and make for MUCH easier prototyping.
Very hard to beat the mini breakout though - with it's build in battery charger etc it makes the perfect embedded MCU after you get all the phy pieces together.
Without knowing for sure - a reasonable assumption is the creators did not see a bunch of GPIO based prototyping using this board and rather as a more permanent GPIO set up. Once you have the prototyping worked out - just solder in the the pins needed.
You could also use a ribbon cable arrangement emerging from Edison and mini breakout boards sandwiched using the 70pin connectors - similar to the sparkfun set-up. but in the end with all the level translations, voltage regulating etc - I find the sparkfun much more flexible (so far).