Yes, you can use Quartus® II Transceiver Toolkit to test the high speed transceiver links between two different devices on two different boards. For example, you may have two different boards with two separate Stratix® IV GX devices, interfacing with each other through backplane HSIO links. You can test these HSIO links using Quartus II Transceiver Toolkit. You will have two Byte Blasters (e.g) from two different boards, connected to the same PC running Quartus II software. Two JTAG interfaces will show up in the Transceiver Toolkit. You can select TX on one device/board and RX on the other device/board to test the link.
Quartus II Handbook does not clearly state if such configuration is supported. This information will be updated in future Handbook version.