These are valid points. The compile only use case is just one of many in reality. Future stories will more appropriately address this. Right now we see compile only dependencies as a strict subset of the multitude of use cases that folks leverage "provided" for.
For all intents and purposes this is because we consider tests to be a consumer of the production code. That means it's interaction in terms of dependencies should be the same as the runtime environment. If I am publishing a module that expects a dependency to be provided by the runtime environment then the test runtime environment should also be required to provide this explicitly. In many cases the "implementation" will simply be the API we compile against plus mocks. However, there's no reason your tests couldn't run against a different implementation.
The IDE integration issue is not a new one. Mapping 'compileOnly' to 'provided' is simply an approximation. Eclipse is even worse in this regard as it doesn't even have a separate testing or compile/runtime classpaths.