Regarding the CAN bus, to some extent, there's always an aspect of star topology on the bus—but traditionally the stub length is short, possibly on the order of a couple of millimetres (in the case of a direct connection to an integrated CAN transceiver). Barring any strange internal arrangement on these controllers, if you leave one pair unconnected, you should still be able to make the connection downstream to the remaining pair, but your stub length will increase.
Here are some general suggestions for optimizing stub length, given other parameters.