Elum was originally planned to be Abe's companion. They would have started out in Nature and been captured by the factory. However due to several plot changes, he was made into a side-character.
The Elum story is quite strange, because he takes up a lot of processing power. This is why you only see him in very linear areas.
Alf jokingly said that Elum was retired and is hanging out around Mudos. In Vykker's Labs in MO you can see some Elum carcasses on an operating table, so you can choose to believe what happened
The bees and honey thing was to replace another way that Elum used to be trapped. So it might not necessarily make sense... but it did make Elum more likable.
Interaction in this game mainly consists of Abe interacting with everything else. You'll find there isn't a lot of Slig-Mud / Mud-Scrab interaction in this game.