Issue with Shimano Di2

Seems like the Shimano was not reporting the front derailleur information due to the missing cable and the Edge was simply showing the result of this.

Without see the actual programming code for both the Garmin and the Di2 here is my guess.

The d-fly is sending out a beacon with the gear when you shift. It's either comprised of two different data sets one for front and one for rear or it's a combine data set. The Garmin is expecting both before it'll update the data field regardless if that field is only displaying the rear gear. The Di2 though isn't send the data set for the front derailleur. So the Garmin doesn't update the display because it's waiting for the front gear data set. It eventually updates because something else is triggering the display update. Possibly a timeout or one of the other sensors trigger a full display update at which point it updates the rear gear displayed.
When the front derailleur is connected even when not in use the Di2 is sending that full data set via the D-fly. I know the Di2 sees the front derailleur because when it's plugged in its showing front as in lower gear whereas when it's not plugged it it doesn't show anything for the front at all.

Annoying is what it is. I don't know if people are having this same problem with the XT/XTR Di2 which you would more commonly see run as a 1X setup but it is an issue with the Ultegra which is what I have.
Right now I'm running it as a 1X because I installed a Bafang BBHD so I'm unlikely to run dual chainrings at least not until I get motivated to machine a front derailleur adapter to compensate for the chainline of the Bafang.