I have complete control over my phone (baseband and userspace), including a nifty tool sanctioned by MediaTek to insert arbitrary AT commands in my processor at will.
I also have the ability to toggle something on the range of 75 GPIO pins. I'm not entirely sure what they do, so I don't play with them. But aside that, I have complete control over every part of the hardware.
It sounds like you don't really have access to that and can e.g. change the protocol messages being exchanged by the BTS/NodeB or the mobile switching center.
Would you further provide the name of the mediatek tool ?
I didn't like the samsung-esque install of their base, so I recompiled to what I liked.
Baseband processor is separate core that runs its own, realtime OS, that handles radio communication. These OS are not opensource.
The application processor talks to baseband via RIL (rild in Android), which is basically a form of IPC via shared memory.
To recapitulate: In your phone, there is another CPU, with closed-source OS full of bugs, connected via air to network and it has full access to RAM of your application processor.
I hope that it's obvious, that it does not matter, what OS runs on the application CPU.