Just like padlocks, replacement ignition cylinders come with a specific key. That's your black key. I think you already know how immobilizer keys and transponder chips works etc.
IMO, the only way that you can have ONE key to start the car and open all doors is to replace your Ignition cylinder and ALL your door latch hardware with one kit. More likely an expensive dealership visit.
I honestly don't know anyone who's done that but know a handful of people that has a different key for the doors and ignition like you. Cylinders and keys fail over time from wear and tear without warning. Happened to me years back on Thanksgiving day.
My SC came 1 alarm fob + 1 factory key only.
Here's what I did:
The remote fob I got from ebay did NOT work. After some research, I got these -
Apparently, the fob FCC ID (OUCG8D-344H-A) has to match the remote brain module of the car. Last letter "A" are the fobs and "B" is the module below (located under the dash above your left knee, while in the seated position. It has a green plug).
Here's how to program the remote fobs.
NOTE: You have to program the new fobs AND the old one together. Initially I can only get 2 remotes to work but after a few more tries, I got all 3 working.
I didn't get a spare immobilizer key. Tho, research also confirms that Ace hardware offers better price, key-cutting and programming, compared to the dealership. You said you already have one on order.
For about the same price, I installed this key-less, push-button start kit that comes with 3 key tags. So now, I have 3 key/fobs and only use remotes to lock/unlock the car.
Normally for the E, a 2nd push on the button unlocks the rear hatch.
Ghost Key - Plug and Play Push to Start Conversion Kit for Honda & Acu
If I was in your case, I would hide a 'lockout" key somewhere outside the car to have access if there's a lost/fail remote fob.
Hope that helps.