I like the idea that Sutekh was just floating around the vortex. Otherwise, you run into problems wher Sutekh's present like... Why didn't Borusa ally with Sutekh against the four Doctors in "The Five Doctors"? Why didn't the Time Lords make use of Sutekh during the Time War?
I keep thinking about the bi-generation and the duplicating of the TARDIS, though...
The TARDIS is a complex space-time event. Maybe Sutekh had always been there, but the TARDIS had been able to imprison Sutekh within its 26-dimension math... until
Fifteen took a mallet to it and duplicated it.
Alternatively, just as the TARDIS told Eleven she took him where he needed to go, it's possible that the TARDIS didn't let Sutekh out of its imprisonment within its complex math until, in her judgment, the Doctor needed her to.