Sounds like your new exhaust is not meant for an automatic VE SS at all - I guess most of the special devices to stop vibration and noise in 4 cylinder mode have been totally removed plus the whole thing has been second guessed to sorta fit the bill as a dual exhaust for a Holden V8 but nobody took the time to factor weight and balance to sit quietly on the mounts like it should (or bugger all else apart from how it looks on the brochure).
I'd make sure there is at least the mandatory flex joints front and rear. Bottom line is the aftermarket system is likely way too short to muffle the primary harmonic, which at 50hz on an otherwise stock GenIV 6.0 occurs 1.5m beyond the length of your car. Your options are to fit HSV bi-modal system for $450 and no more problem, run 1.5m capped pipes to cancel that frequency for about $450 but that's quite a bit if plumbing each side underneath, or replace the tune with custom OS from eBay for about the same and probably end up with a tune that puts a smile on your dial (YMMV).
About V8s and fuel, if you are just putting around the burbs hardly drive 20,000k a year then I agree, no point whinging about fuel use or price, you will spend more on tyres and servicing. However it you really drive your car like it's made to, once your annual fuel bill gets well into five digits you'd need to be a mug not to get the most efficient use from the car, your money and the fossils you burn.
