RMA of unlocked/rooted Nexus 4

I have already RMA'd my Nexus 4 which developed a problem that is chronicled in another thread.

So a replacement is on the way, but I recall now (lol, I know...silly me) that I unlocked and rooted my Nexus 4 (how else would I get a decent backup?). An Android guru at work told me I shouldn't have any problems with Google throwing a hissy fit over it so long as I restore to stock the recovery and the ROM and re-lock the boot loader. There seems to be a "1-click" option for this with the Nexus 4 Tools.

But surely Google Play Store still knows (on some level) that my current Nexus 4 is unlocked/rooted. I have installed Play Store apps that only work if the device is rooted.

Do you think I'll have any problems with Google Play Store denying my return given my current situation? Is using the Nexus 4 Tools the best way to go about restoring to stock?

Thanks for input.