You can have an overlapping jib on a roller furler. Normally the battens will be rotated on the sail so they are parallel to the luff (they get a bit longer too - usually). This way they are parallel to the furling action and will roll up with the sail.

With regards to it catching on the spinnaker halyard - it takes a little effort to either furl after the spinnaker is up (and has some air in it) or make sure the spinnaker halyard is somewhat taught before you start to furl the jib. Furling jib with a spinnaker is a pretty common setup...it just takes some additional process to make sure everything works reliably.