My suspicion is that this works in maven projects because m2e provides its own Eclipse builder that copies the resources using some maven mojos that get run as part of the Eclipse build cycle by m2e.
M2e tools integrate deeper with maven than gradle tools do with Gradle. Presently there's really no mechanism for gradle builds to participate in IDE builds and 'play their part' so to speak in the Eclipse builds lifecycle. So instead we have to emulate Gradle behavior by mapping it onto equivalent Eclipse concepts.
When resources folders are treated as 'source folders'. The Eclipse Java builder handles them correctly, copying non Java resources to the output folder, but, as you noted, it renders a bit oddly in the package explorer view. This has never really bothered me personally.
It may be possible to fix this somehow, but as a first step Gradle itself would need to refine the tooling API model it exposes to the tools to distinguish 'resources' folders from 'source' folders. Right now short of implementing something hacky based on the names of source folders, the tools have no way of knowing the difference between a 'real' source folder and a 'resources' folder.
So the tools really forced to treat them the same.
To be honest with you, it looks like fixing this is not so easy. And it doesn't seem important enough to warrant a large effort.
The problem seems mostly cosmetic. In a sense, actually seeing them as packages may even conveye some useful information, i.e. that those things are indeed on your classpath and accessible via the classloader.
Kris De Volder -- SpringSource