It's got nothing to do with the factory or homologation rules......they are totally independent from the factory even though they are the gearbox suppliers.
Would this "aftermarket" type change be classed as a major modification sufficient to cause issues in some countries?
This was my thought.
Clearly the Morgan was homologated with a manual gearbox and, at the very least, a change of gearbox would effect consumption and emissions figures.
When I bought my car various items were fitted by Aero Racing as aftermarket changes. I was told this is because the car must pass through the factory itself in the form in which it has been homologated because they could have an inspection at any time.
In reality with the small production and customised nature of Morgan cars it is very unlikely that any in depth enquiry would be made as to whether or not a particular gearbox was in the homologation as a model variation.