IMO, My device is not "secure" unless I can control the device's OS & inspect the device's hardware. My phone, my router, my PCs, my GPS, all have firmware I've compiled myself.
This doesn't make it secure. It just means that if someone's made a mistake, or inserted a backdoor, you've missed it. Control != Security -- sometimes it just creates a poor illusion of security. If you don't have control, you have to trust someone to provide security. Depending on who it is and what their experience is, I often prefer to trust.
Regardless, one of the big issues that I've seen in this area is that although yes, you CAN jailbreak iPhone or install custom firmware on whatever device you want, you want the ability to deploy commercial-off-the-shelf stuff to users in the field with a 10 second install from the app store. They want to leverage the existing distribution network for the product and application distribution for software packages. They want to piggyback off the commercial world with minimal development effort and cost. What you're proposing a better model from a secure perspective, but is massively more expensive.
The shortest distance between two points is under construction. -- Noelie Alito