I thought if there was no HDMI on the rPI, it wont initialize the hdmi port at all. Or is that just the BBB?

Regardless, if you have a monitor connected to it, I’m sure you don’t need the rPI in the same enclosure as the OS. Have you considered using your own enclosure for the rPI and use a ribbon cable to and from the OS to the rPI through the LCD hole? that would free up a lot of access to the rPI and not clutter up the inside of the case. If you consider connecting a backup camera screen to the rpi, you can leave that in the same area as the rpi/os, and have a nice display that can possibly have some nice graphics or just a simple ncurses based app showing the current status of the rPI, like htop?