I can see what you're getting at but none of that precludes tools being provided by MS that has direct access to low level instrumentation and data from the hypervisor and provides a mechanism that allows the user to get to that information without MS handing over the keys to the hypervisor.
I agree that it's not going to be a full blown dev kit but I do believe that MS will provide enough tools to allow you to develop full blown indie games on the device. There would be no point otherwise.
Proper debugging does involve handing over keys to Game OS and Dashboard OS, as well as at least portions of hypervisor unless added hardware is provided. Which is why it's normally hidden behind restricted distribution and a nominal fee equal to the cost of several games; hell, even full rather than restricted TEST access requires playing burns of retail games, so sans restrictions the box needs to be at least $1000 or so to keep people from just treating it as an up-front purchase of every game on the platform. ;P
It makes far more sense as one of three alternatives:
a) Limited to no debugging or other direct hardware access, intended as an aid for rapid prototyping. You get the opportunity to get your title started, and have something to show while you apply for a full kit/see how quick and easy it is to port your PC title.
b) Ability to run limited software under Game OS; possibly a service to sign your software (pending review in some cases) and authorize it to be run on your Xbone, which would make total sense under the old always-on paradigm.
c) Dashboard OS being yet another Windows 8 device, with all that entails.