If JLC would allow any customer to 'upgrade' their watch to effectively convert it to a version that is a limited edition, then they would be unloyal to those who have paid to buy the watch from the limited edition, as some of them might specially have decided to buy the watch because they though it was more exclusive.
Plus, from a commercial point of view, the marketing is supposed to introduce new products which are attractive, but also make the former products obsolete, so in a way create a new demand among clients. If you allow the clients to 'upgrade' their watch, then you just cut the branch on which you sit.
I can see how this is frustrating, but this is just the way it is.
The solution would be to go for aftermarket parts (as per the chrome wheels you can put on your car if you wish to do so), and from that respect, JLC would have no word to say on that, as as the legitimate owner of the watch, you can do whatever you want with it after you purchased it. But I doubt there will be a maker for that kind of very specialised technical / limited demand part.
To take again your analogy with cars, if you buy an Aston Martin DB7, and then when you see the limited DB7 Zagato and you want to buy the parts to 'upgrade' your car, I doubt they will cooperate.
That might be sad from a customer perspective, but this is just the way business works.