You're right. Here's the response from the Hsu support team.
I just spoke to one of our technicians, and he thinks that the best way to
hook up the VTF-1 would be to run the speaker wire from the subwoofer
output to the left or right high level input on the VTF amplifier. He said
that it is not a good idea to run from a high level speaker output to a low
level rca input, as the input board could blow that way.
The reason the Onkyo receiver was designed this way is probably because
the subwoofer in the Home-Theater-In-A-Box system is unpowered, so the
Onkyo receiver is actually powering the subwoofer in addition to the
speakers.