These are things that would have been expounded upon had the web series continued, rather like the way the events of the Time War were slowly teased out of the Doctor in the new series. When it was dropped (apparently before Shalka was even broadcast), we were left dangling.
*However*
Paul Cornell, in Chapter 6 of his novelisation of the story, gives us a heavy clue as to the origins of the android Master.
***SPOILERS***
"The Master had grown more desperate and ruthless as time had gone on, using up his natural ability to replace a dying body with a new, healthy, one, and having to move his consciousness into increasingly more complicated host forms. The Doctor had still beaten him every time they had met.
But now they travelled together, thanks to the events of the last time they had encountered each other. It was fitting that they had ended up, however awkwardly, on the same side. Fitting, but still somehow frustrating."
The "last time" was of course the TV movie. Thus it is implied that when the Eric Roberts Master was sucked into the Eye of Harmony, he became a part of the TARDIS and that (presumably) the Doctor has constructed an artificial body in which the Master's consciousness is able to interact with the physical world. However, since this consciousness has now merged with the TARDIS, the android is unable to leave the ship. Obviously, the Master is not entirely happy with this arrangement (note when he tries to hypnotise Alison before the Doctor interrupts), so one could assume he'd probably try to escape eventually.
But of course, we'll never know for sure what was to happen!
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