I suspect that most companies that deploy a free software based stack will lock down basic functionality. Having a phone based on free software doesn't necessarily mean that you can modify the software on it. (GPLv3 takes a stance against this, which means that anything you want to lock down can't use GPLv3 software.)

Motorola have been using Linux on their phones for a while:

http://www.news.com/2100-1001-984424.html

However, this has not translated into any additional freedom for Motorola customers.