Thanks so much for your input @gr5, @ahoeben!
I just combed through the manual and original documents that came with the machine and I couldn't see a EULA or find anything on the website in regards to the machine and the firmware (I found warranty for the machine and licenses for Cura, but nothing for the firmware). I have an S5 on the way, so maybe they have updated docs with those, but I'm 95% sure there was not an "I accept" button when I first started the machine. I also can't find anything in the menus themselves.
This is how I had been planning to set up the install, I don't want to modify the ultimaker closed source software if thats not allowed, I can probably just run my stuff alongside it and access the open APIs when needed. Debian is open source, and so is the marlin that runs on the ATMEGA chip, so modifying those should not be an issue. If the UM firmware is based on marlin, it would inherit the GNU GPL v3 licence— that's why I think they understandably offloaded some of the proprietary functionality onto the Olimex. But that also means the firmware itself should be modifiable and redistributable.
I would really like to hear from them before proceeding too far as I understand a lot of work goes into developing IP.