I emailed Google and asked on their chat line these questions. Here are their responses:
There is only one difference between the Verizon variant and the Google store variant
i.e the device with the Verizon will have a locked bootloader and Google store variant device will have an unlocked boot loader.
Here are the 3 apps which come installed with the verizon variant devices. my verizon, meesage + and go90
Yes, there are these three apps which will be pre installed and the boot loader will be locked. Other than this there are no other changes between the verizon variant and Google store varirant.
I can only assume this is factual, but it was direct from a google rep.