I just bought a Xperia Z from T-Mobile myself today (Blackberry Trade in Promo, $6 down!) and was just literally talking about this very concern.
I'm going to bypass the Bootloader Unlock and attempt a root/recovery without unlocking it. At that point there shouldn't be an issue with flashing a custom rom. As long as you can flash back to stock (stock recovery, stock firmware) you should be fine. There seems to be a handy "flashtool" in one of the stickies that will explain how to do this.
I imagine you at that point should be fine. I would advise: do not unlock your bootloader. Most OEMs (I worked for HTC for many years) watermark your device and it's a pain trying to remove it.
Worst case scenario you can always do a warranty exchange to get a fresh device before JUMP upgrading later.
You cannot unlock the bootloader on the C6606 anyway, so therefore you cannot run CM11 (or any CM/PAC/AOSP/AOKP based rom) as running the custom kernel it requires needs an unlocked bootloader. The most you can do is flash stock based custom roms.
To verify this for yourself, enter *#*#7378423#*#* in the dialler, then look in Service info -> Configuration. You will see that it says 'Bootloader unlock allowed : No'.
When you need to return the phone, just flash a stock C6606 FTF with Flashtool and there is no way they can detect that you rooted it or flashed another rom.
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