Funny, I have the opposite experience in Switzerland:
I had a busted micro-USB socket on my Xperia X phone (so I couldn’t easily connect to flashtool and return it to factory state. In fact I couldn’t even charge it).
Warranty-repair subcontracting company explained that they don’t give a damn what’s installed on the phone:
they will always wipe the phone, flash the factory image and relock the boatloader as part of their standard repair procedure (to cover troubles which are of software origin I presume? Or just to be sure the technicians will find the standard self-diagnose tools in there?).
And it’s the responsibility of the end user to back their data up before sending and then restore them upon return.
(Luckily in my case, everything was perfectly backed up with rsync over Wifi before. One of the small joys of running a full blown GNU/Linux on the phone).
So it proves that it’s pefectly doable for a company to service hardware trouble on a rooted phone.
I would also suggest going to a consumer rights group (luckily we have those here in Europe).