hello
the latest version of the board has a couple more resistors in series with the tx and rx pins of the microcontroller. this was supposed to make it easier for people to reuse the pins when the serial port is not needed.
that's the only difference.
the multisensor board has been built and used in a project. we were thinking about selling it but there is so little time and so many things to do. In the end it's only the 4 of us who are doing everything. anything we sell needs to be supported and this particular board requires a lot of explanations. when we have time to write a manual we'll sell it
you can access the microcontroller at any level if you know how to 
the arduino code is C code. if you write a c statement anywhere it usually compiles just fine. so if you access the right registers you can turn on the pullups and the rest.
internal timers are useable. just be careful because if you use PWM or other functions these also use the timers and it can get messy. details are in the source code you can browse on Arduino Starter Kit kaufen [verschiedene Ausführungen]
the serial port is connected to the usb interface chip so most of the time it's hard to use the pin for other purposes
in theory before you call beginSerial those pins are not used by the serial port yet
normally the serial port is the simplest and cheapest way to do debugging. remember arduino tries to be easy to use for a beginner.
it is possible to use a regular pin for serial transmission. we will release the code soon.
sorry for the quick anwers but I'm overworked 
massimo