attachInterrupt() is not supposed to be a high-level call. It is only supposed to do one thing, attach an interrupt. If the hardware requires more, then it is the programmers responsibility to supply it.
To answer your question directly, I think it is not relevant, in how many cases are extra steps required to make a fully functional interrupt. It just needs to be documented properly.
To require such a basic function to clear flags would both hard code an action that some programs might not want to use, and also create a maintenance nightmare as every implementation of it would have to be continuously vetted and updated.
Keep in mind, it's happening because of a hardware dependency.