They said there was no other way to route it. Immediately following that we cut up the piping ourselves and routed it the way I actually wanted it, without changing anything on the car and using no extra piping except for having to buy 1 donut of pipe.
When we mounted the intercooler we left enough room behind it to run the piping through, but the Fyshwick guy ran it under the front of the car (in front of the tow points, probably wouldn't have passed rego) where it would have been smashed the first time I got too close to anything like a kerb. And the pipe was just hanging there with nothing except the joiners to the other pipe sections holding it. After we finished it was a LOT more secure.
Pic A - when the shop finished with it
Pic B - when we finished fixing what the shop did
Bear in mind this was over 5 years ago, things change, and as I said, the exhaust itself was great.