Versions:
MineFactoryReloaded-[1.10.2]2.9.0B1-222.jar
natura-1.10.2-4.1.0.72.jar

As I mentioned here: skyboy/MineFactoryReloaded#604 (comment)

Is that an issue, planned feature to be added back in or ... ?

Reproduction steps:
Place planter, dirt on top, power it, put Natura sapling, e.g Eucalyptus into it, nothing happens.
(Should plant it on the dirt above)