The fact that this issue has been around for nearly 4 years is pretty much the opposite of "The sweet spot in between standardization, declarativeness and necessary flexibility."
The comments above have given various examples of good reasons for the "provided" scope.
My current one is the implementation of a javax.servlet.ServletContextListener, i.e. the classic servlet-api dependency for which providedCompile and providedRuntime has been added to the 'War' plugin.
Yes, I've been able to solve this by means of https://github.com/spring-projects/gradle-plugins/tree/master/propdeps-plugin - but it's quite intrusive. I don't think that 'idea' and 'eclipse' configuration should "leak" into the build file. It seems to work fine for me but Tilos comment directly above mine isn't exactly reassuring...
I frankly don't understand why you insist that this shouldn't simply be added even if you'll come up with a better approach in the future. It wouldn't be the first deprecated feature and definitely won't be the last either.