Looking at that diagram, it seems as if all the pins are predefined for a specific use. Are there open pins that can be programmed?
RPi3B+ uses GPIO03 for power on / shutdown. That pin is also predefined for I2C SCL (I2C clock), but I2C will only be activated by a dtparam at config.txt. I bet your Le Potato uses something similar to activate I2C. So I would use I2C_SCK_A0. SCK probably means SCL here.
...switched HDMI ports and then configured Kodi via the GUI.
That probably creates a setup error. Login by SSH, delete .kodi/userdata/guisettings.xml, reboot, and configure again.
Try an HDMI cable, which is known to work with 4K. When buying a new one, it should have HDMI 2.0 or 2.1 standard (a.k.a. 4K).
Current RPi prices are so crazy that I had to spend some hope. 
RPi Zero W might work for your needs: Click!
If you find a regular (non-Android) Linux for Fire TV, then you could autostart Kodi on it.
Don't expect better performance on LE. Android is already super optimized for all popular media, and Kodi app uses those API's.
To make it perfect: Cut a larger prototype board to make it fit into your desired case. So you can drill mounting holes at the right spots.
I would use a single-side prototype board to put everything together. Example: Click!
Use the non-contact side to glue your PCB's on (hot glue gun), and use the contact side for the wiring.
Kodi app is available for Fire TV stick via sideloading. That's why an LE implementation is very unlikely, and doesn't exist yet.
Not sure about your current wiring now. If not already done, try:
AUDIO: HTPC HDMI -> AVR
VIDEO: HTPC DP -> adapter -> projector
Play around with different pass-through settings for this setup.
The specs at post #47 mention "Intel Clear Video (HD) Technology". If you find switches for that in the BIOS, try different settings.
Name it OPi and RPi to avoid confusion.
Do you use AMD or Intel graphics card?
I answer to myself: It's this Intel processor graphics.
Did you had a look at BIOS / EFI settings? Maybe you'll find a tweak for DisplayPort.
While playing Atmos, did you had a look at "Audio and subtitle settings", which is part of the playback bar on the bottom. That menu also has an "Enable passthrough" switch.
What's the "Passthrough output device" on LE settings? Do you have multiple choices?
Because GUI sounds are affected, try to play Atmos with disabled "GUI sounds" on LE's audio settings.
Do you use AMD or Intel graphics card?
What do you need from me?
Well, you could spend money.
What do you need from us?
What do you mean a current nightly? Sorry for being so dense...
That's progress. It makes me thinking, it's not a software bug, but the HDMI cable (NUC -> AVR). Bugs usually don't behave like this.
Maybe it was working on Win10, because you had a lower screen resolution. This reduces the HDMI data rate, so there is enough room for Atmos data.
Try another HDMI cable, which is made for 4K (HDMI 2.0 or 2.1 standard).
