Goomph has this logic:
https://github.com/diffplug/goomph/blob/36ee3412d39662e5b8ac659150e805b2d1119887/src/main/java/com/diffplug/gradle/eclipse/MavenCentralExtension.java#L120-L137
With P2Deps, it seems to be that maven transitives are being resolved using maven rules, which results in transitives getting bumped to newer releases if possible.