Hi Eric,
I'm sure you can make a specification at the factory. I specified and bought my PlusFour from a German dealer.
When the car was under construction I flew to the UK to do a factory tour in Malvern and see my Morgan under construction. After that visit to Malvern I have always thought the following:
If I were to buy a new Morgan again I would do the spec in Malvern.
You can see all the options there for vehicles that are under construction. Colors, leather, etc. are visible to a much greater extent than at a dealer. However, you will certainly only be able to order from your local dealer.