@procount What. A. Coincidence! 
I was reading about PINN earlier this week so that I could produce appropriate boot and root tarballs for PINN. Thanks for making a start on this 
If you've got any tips for me the create what you need, do let me know!
I switched to using labels to follow the convention used in the new Ubuntu server images, and it also made USB booting work without any manual tinkering by users. Sorry if this has caused you a headache.
As for uboot.bin, this is installed by flash-kernel which is used to configure initrd for the custom Raspberry Pi kernel used by Ubuntu. As it happens, I don't use uboot in 18.04 but instead, use the traditional boot loader because uboot has different binaries for Pi 2 and Pi 3. That would require I make/publish multiple images and something I want to avoid.
I'm working on beta2 images today, I'll see what I can do to clean up uboot cruft from the image. That said, when a kernel update is applied flash-kernel will deposit uboot in the appropriate places but this will not be an issue for PINN I think?
Thanks for getting in touch, I am keep to make sure Ubuntu MATE 18.04works well with PINN