I think I can see what's happened here, putting my configurator builder hat on.
1. If you look at an actual image of the Super 3 logo stitching you will notice that it's a negative stitch pattern. The 'Super 3' isn't stitched but rather the areas around it. Having this in contrast would look horrible and only really works as a blind stitch. Blind being the same colour as the leather.
2. Taking point 1 into consideration, production likely decided to offer just the one option of 'blind' emblem so that regardless if one selects the wings or 3, the trim shop knows what to do.
3. This wasn't fully communicated to the configurator team and treated the Morgan wings emblems as they are for the rest of the line up.
I know for the cars we build, production needs an option code on what emblem and it's colour state, Blind, Contrast or a fixed colour. It would never be a single code of 'emblems'
This of course doesn't help you whatsoever but thought I'd shed some light on what might be at play.
If it helps, many ultra luxury and sports brands do offer a Blind option for emblems and you would be surprised on how many pay for this vs. a Contrast.
If it were me, I wouldn't want that part of the leather replaced just in case the batch they replace it with is different. I also work in leather and also see it in the factory I work at. Not all hides match one another and even the pigment can be ever so slightly off. I'd ask for a refund of the option and a goodwill gift for the trouble. Again, just my personal view
Thank you very much Perry for the insights and explanation. I will consider having to live with my "ultra luxury" Super 3

- but first I want to get some insights how the customer service at Morgan is "ticking" i.e. how the dealer response will look like

I am a new customer to Morgan (having owned many different car brands) so I am just curious to see how they deal with IMHO justified complaints. It is really not about getting a "discount", more of a principle. If they proud themselves to have "the most configurable Morgan ever", then please deliver on the promise. Having said all this, I am still full of excitement and joy when I look forward to picking up the car.