I'm just wondering if something has been lost in the detail here.
Programming source code, or making alterations to source code has to be strictly controlled. It’s recognised across the IT world as an essential element of good control and governance. There has to be a gate keeper, who checks the alteration, tests it in isolation, before allowing the change to occur. It is the foundation stone of ensuring that the systems work effectively and without bugs.
If you have all or one of the partner nations making alterations independently, then those aircraft will then have to be treated as independent entities as new central ‘updates’ will no longer be guaranteed compatible. It makes sense to have a central code processing centre.
To guarantee independent action, the UK would need to have assurance that it has the ability to make and process alterations whenever it wants, without asking permission from the US. This might mean that UK coders are integrated into the processing house structure, and that the UK retains a cold site within the UK which is capable of undertaking the work. In the event of a crisis, our coders can start up at the cold site, and make whatever alterations we choose.
Perhaps it is worth seeing the F35 as more akin to the iphone when O2 held the monopoly. We might be happy to join the ride, because you get a very slick product, with a huge support structure driving, and access to fantastic apps. But if your relationship with O2 turns sour and they start hitting you with huge bills, you want to know that you have the ability to ‘jail break’ the phone. But its probably far better to stay on the train, and work together.