It often occurs that you need to include a set of common definitions that are supposed to be known to all files while building a library. For instance, I'd like to test against TARGET_OS_IPHONE everywhere in implementation files. The only alternative without a prefix header is to manually #import <TargetConditionals.h> in every single file, which is both error prone (test can silently fail if forgotten), and tedious (repetitive code). Like, adding #import "common_prefix.h" to tens or hundreds of .c files.
About the replacement with a module, I agree that, with caching, they efficiently replace precompiled headers when they are used as a speed optimization. But my use case is not about speed, and I don't see how modules could help solve the issue here (can you give an example of what you have in mind?).
Now it is not that I'd absolutely want a specific setting. I'd be fine with generic "safe" flags that would let me use this package as a dependency to other packages, as there's nothing unsafe about importing a file that resides in the package source tree. That being said, if it's very often used, a dedicated setting could well make sense.