You're (understandably) confusing two different things which were both referred to as a Time Vortex.
The hole in space time which made The Master go crazy is called the Untempered Schism, which is described as follows in The Sound of Drums:
a gap in the fabric of reality from which can be seen the whole of the Vortex
The energy inside the TARDIS is The Heart of the TARDIS which is the living essence (mind, soul, etc.) of the TARDIS itself. The effects of contact with this aren't very consistent:
- It turns Blon Fel-Fotch Passameer-Day Slitheen into a baby in Boom Town
- It infuses Rose with god-like powers of time and space manipulation as you mention
Though this also caused Rose fatal damage, which she was only saved from by The Doctor sacrificing himself to remove the essence from her and place it back into the TARDIS. The fact that this killed The Doctor and caused him to regenerate suggests it would probably be fatal to a single regeneration of a Time Lord too.
Though it's equally possible that the TARDIS intended to punish the Slitheen as she intended to kill the TARDIS. She may have also intended to use Rose to save the day by giving her the powers, but killing her was an unintentional side-effect. These ideas would be backed up by the fact that the TARDIS is sentient (as indicated in The Doctor's Wife), and would then lend credence to the idea that the TARDIS may not do anything to a Time Lord who means it no harm (as the TARDIS would know, being able to see all of Time and Space).