I did my own installation in an XR4040C. I can see why LS recommends having the dealer do it - not an easy task. The smart money says remove the roof which would require at least two people on ladders. But it exposes everything and makes installing a radio bracket easier.
And as a side line - you can insulate the underside of the roof while it is off(wish I had used this method).
Also, I would recommend removing and discarding the stock speakers, they're useless. I replaced them with Kenwood 3 in 1 speakers. True they're still 4" and don't carry bass very well but I'm happy with them.