Hi Daniel,
Sorry you had to wait so long for the answer.
Of course you can install a full desktop ROS version on our Ubuntu image if you want to however If you want to use the standard Ubuntu 16.04 you will have to complete couple of steps to make communication between SBC and CORE2 possible.
Type in:
sudo su
and next type in this command:
wget https://files.husarion.com/repo/repo.key -O- | apt-key add -
echo 'deb https://files.husarion.com/repo/ xenial main ros' > /etc/apt/sources.list.d/husarion.list
apt-get install -y apt-transport-https
apt-get update
It will allow you to install all Husarion pkg.
You need to install husarion-sdk pkg so you have to type in:
sudo apt-get install husarion-sdk
Answering your next question- no, you can’t do it using RPI connector because it’s busy however as you mentioned, it is possible to do it via USB cable. You can find more information on how to do in this topic.
In case of any other questions feel free to let me know 
Regards,
Hubert.