Well, I think you could have gone by with just a MightyHat. That is a more elegant gateway board that has the same functionality and plugs right ontop of the Pi via provided tall header, has a gateway sketch sample to use with the onboard radio of your choice (code sample for RFM69 only), plut it's very compact compared to the MBoost combo and requires minimal soldering. The MightyBoost sketch only handles the PSU brains for MBoost, not the gateway part. Basically the MBoost is just a booster that allows you to control it either via a jumper, or via Moteino (which gives you more features and ability to make it behave like ATXRaspi).
Now that you have all this hardware you can make it happen, just like you said, and i think you're on the right track. It will be more soldering and wiring and sketch uploads but it will work, that's how I ran my gateway for about 2years+. That being said, you could use the MBoost for other similar projects where the Hat will not be suitable.
MBoost will not need taller than regular headers (female + male) to have enough clearance between Moteino and USB-A output.
With MBoost you will not be able to integrate the gateway sketch with the MBoost sketch simply because you will not be able to control the output across power cycles. The MHat has a special feature that allows the PSU to operate independently of what the atmega328 does (or if it freezes, resets etc. This is because the Pi is critical to keep going if something bad happens on the atmega328 side. Hence you will need a separate Moteino for the gateway part in a MBoost combo.