Rather than placing all the rubber tree saplings next to one another, like it does with other types of sapling, it plants them two blocks away from the farming station and with one block of space between each sapling.

Is this intentional—and if so, why?

I think the IC2 rubber trees need the space for the rubber "spots" to generate.

They’re on the log blocks themselves, though. Why would it need more space for that?

After talking with the IC2 developers it appears there is no requirement for spacing the trees apart.

It’s only possible to automate the production of sticky resin using Ender IO’s farming station, but you won’t get rubber wood or rubber wood saplings.

I’m not sure whether this is intended, but I don’t know why this would be a feature.