The point is that if the code is inlined into your application, you'll never actually be accessing the functions in the library installed on the system (because the code was copied into your app).
This is also true for some existing parts of the standard library, but because they are required to be ABI stable, they can never be optimized or improved in a way that affects their ABI (e.g. altering function parameters, struct layouts, or internal side-effects).
And yes, it's absolutely a problem. The cost of stdlib ABI stability was that some mistakes can never be rectified - there are bad API decisions or poor optimizations that we are now stuck with forever - but ABI stability was the necessary price for every Swift app not having to include its own copy of the entire stdlib, and the ability to have Swift APIs in the OS instead of being forever stuck with Objective-C.