Funny I was just thinking about this, or at least something similar, earlier today
In answer to your question, IMHO, it isn't necessary to integrate a standlone ECU in to this. I don't know if there are enough people running a standalone/piggyback ECU to warrant the extra effort. I'd say 99% of tuned cars are using Uprev, or EcuTek. Which work with just a cable connection. So a USB port is all that would be needed there.
My though is that the value of this for those of us who are more performance oriented anyway, would be the ability to interface and monitor the factory ECU; through UpRev, Dashcommand, EcuTek, whatever.
Which raised the question: which OS is will this thing be running? I assume one of the main goals is to be able to control this thing via touchscreen. So I imagine Windows 8/10 or Android-x86 are the two logical choices. If I had to guess you are probably leaning towards Windows.
Which is good since you need Windows for UpRev/EcuTek interface. You need Android to run something like Dashcommand/Torque. However, there is an app called Bluestack that let's you run Android apps on a Windows system. Which would give you the best of both worlds in theory.
Running Windows would make it possible to plug in keyboard, and be able to change parameters on the car's display for those of us running UpRev or EcuTek. or for those that aren't running those, you could easily (not yet tested) get it to work with Dashcommand/Torque.
Either way, I don't think you need to modify your design to accommodate anything more than a few easily accessible USB ports (perhaps some tucked away and 1 or 2 easily accessible from the front or the center console).
just my
of course.