The difference is that the operation of the Crypto AG machines was secret. Only the employees of the company had access. The operation of some contemporary systems is available to the whole world in the form of source code. In some cases multiple entities with no particular connection actually work on that source code. The trick is in insuring that the source code is the only thing that contributed to the program you are running.

As a fairly extreme example, consider what it would take to backdoor GnuPG. It is distributed to multiple platforms/OSes, most of which allow anyone to check both the signatures on the source code and then recreate the binaries.