It should be noted that this situation is not all that uncommon at Apple. For pre-1.0 iOS work, e.g., often individual engineers on macOS teams were tapped to do iOS specific changes to their components without their managers having clearance to know about it.
For the Mac Intel switch, the situation was even more curious, as the earlier work was carried out by a larger group of engineers, with little special secrecy, but the final stretch was done by a smaller subset of those engineers in strict secrecy, while the others were led to conclude that the effort had petered out.
The difference in this case was, of course, that the client of the special project was apparently external…
> My boss was told I was working on a special project and not to ask questions.