I think it's debatable. If they didn't want you to touch anything inside it would be in their terms and conditions, plus they would seal the box up so you have to break a seal to invalidate the warranty.
My take on it is why do they supply all the extra PCI connectors inside if you can't use them?
By the way, I recently bought a new computer with no software on it because I run Linux and found it didn't work the HD wasn't found, on having a peak inside they hadn't fitted the SATA cable. I phoned them up and told them, they were very embarrassed about it and offered to take the computer back, I said if they didn't mind me fitting it just send me the cable. There was no question about the warranty.
Have run it up anyway! Might have been a first job for a new member of staff, but like I say to mine on the rare occasions when they moan about workload...The bigger you get, the more personal touch and QC go out the window.
I gave them a call and I guess I've been lucky, they said it's no problem to fit it myself (having explained I knew how simple a procedure it was) Mind you, they're a local independant company, I doubt any of the national chains would be as accomadating.