It's all about the $
Apple will push the "We care about your privacy" but it really comes down to making money. The idea of a company giving away the keys to what some people consider their lifeline would certainly give some people pause about buying a product (even if they are giving away more valuable marketing information to Facebook, Twitter etc through social oversharing.)
Given the push with Apple Pay and using an iDevice for making payments and who knows what other financial services in the future. If they desire to replace ATM's, credit cards with an Apple device (and essentially act as a financial service provider) it would be that much harder for them to sell those services to both the industry and the consumer if they were seen to publicly provide a means to access the devices even in a controlled environment. This is where they are probably envisaging huge profits in the future by getting a percentage of each transaction processed via millions of iDevices.
Even if they presented facts stating the work (if performed) was carried out in a strictly controlled environment there would always be that doubt that they could carry out a similar process remotely on any device. There would also be the worry that a foreign power or criminal organisation would then target their engineers to enact the same process for those parties.