I decided to leave it in. I see no good reason to take it out and the risks of removing it and potentially mixing up the pins during removal or it's reinstallation afterwards, outweigh the pretty much 0 chance they will open up the computer, void my warranty, and later suffer an engine failure within the few remaining months of my warranty.
You can easily disable the JB3 so you can't tell it's there by simply driving it. Plus it's an extra big pain for me to remove since I used heat shrink tubing on the connections.
I'll let you know if I have any problems.
2008 Sedona Red 135i coupe
Black leather with aluminum trim
Sport package, Active Steering