Hey, you have to manual it, or write a plugin to take the portal and kill boss. The current explorebot doesn't account for this issue, hence the beta is in the works and does account for it. Soon.....
Manual means you just stop bot, move it to boss room, start bot and watch it kill. easy peasy.
The bot 40% of the time will go to boss room and kill, if you have a fast enough clearing speed, or you can just set the bot to not leave the instance after X amount of time, it will eventually go to the boss room.