I've seen some pretty nasty "custom installs" from them. eg: exposed wires, making unsused holes in the car, not wiring speakers in phase....
Granted there could be a few "good" stores here and there. I mean, I suppose it wouldn't be too bad, if you watch them as they work, making sure they dont do random things.
You didn't notice a difference when you changed over from the stock to pioneer headunit?
If you have to go strathfield, go and listen to a few sets of speakers for yourself, sony, kenwood, pioneer. The best ones will be the one that you think sounds best. Sony and kenwood I haven't heard, so can't help you. The pioneer tsa1670/80 ? and tsa6960/70/80 ? i've heard. Sounds better than stock, but if they have the tse1695, i'd personally take them over the 1670/1680. 6980 needs a lot more power than from a headunit to really get moving, so it was rather dull and muffled.
As for cutting the parcel tray, i thought it'd be removable? If its not, make sure that whatever they do, they dont just cut a hole and screw the speaker into it, they should make a carpeted, or at least painted mdf backing cut to the right size. Same for the doors.
edit: or you could just buy a phone from them, sell the phone as new, then buy speakers from somewhere else