Still not enough to call this a win for the Xeelee (well for me anyways). How would they counter against the Eye of Harmony and the Key to Time? Those things can change the laws of physics with a whim. The Doctor's outdated TARDIS is shown to be able to detonate itself at every point in time and space. After that, all stars go supernova, all history ends, erasing the universe, basically, it can cause a total event collapse. The place where the TARDIS was, when it exploded, survives longer, being the eye of the storm, but only a few thousand years more. Also here is a quote for it: STARK: All reality is threatened.
CYBERLEADER: All universes will be deleted.
Additionally, I've heard Omega can make stars go supernova with a wave of his hand. Furthermore, there is this thing called The Axis, which is where Time Lords stick time lines they don't like:
DOCTOR: Ah. It's rather as I feared. We're in the Axis.
PERI: The Axis?
DOCTOR: Yes. It's, er, a complex. Look, are you sure you want to hear this? We'll be on our way before
PERI: Doctor!
DOCTOR: Right, well, er, imagine the spokes of a bicycle wheel. Each spoke is a damaged or truncated reality, a sort of dead-end in Time. They're formed by changes in established history, some big, some relatively small, which cause the flow of subsequent events to spiral out of control. Often catastrophically.
PERI: And the Axis is the spindle, right?
DOCTOR: Exactly. The hub that maintains and regulates the truncated realities, and ensures that the contamination doesn't spread to the primary timeline.
ERIMEM: What?
DOCTOR: Oh. Well, it (sighs) It's like cauterising a wound to make sure the infection doesn't spread.
ERIMEM: Yes, I see.
DOCTOR: Now, if you'll excuse me (under the console) let's see about getting us out of here. Really don't want to hang around if we can help it. I'm sure if I just
PERI: Doctor.
DOCTOR: (out again) Yes, Peri?
PERI: How exactly do these timelines get er, damaged?
DOCTOR: Ah. Excellent question. And, well, though I'm ashamed to admit it, the answer can often be summed up in two simple words. Time Lords, who are, well-intentioned or otherwise, prone to dabble and not really tidy up after themselves.
PERI: So. This is all your mistakes tucked away in one big cupboard.
DOCTOR: Well, I probably wouldn't have put it quite like that, but yes, there's an element of accuracy in that description.
-Axis of Insanity
Basically, if the Time Lords don't like a time line, they send it into the Axis. The one the story is all about is one that was sent their after their agent, who was supposed to just clean up a mess, failed to realize the target had Time Lord level tech taken from another universe. The Time Lords just disconnected his entire time line from reality and shoved it into a box. Other time lines accessible from the Axis are a bunch of alternate Gallifreys, that feature in the audio series Gallifrey. Most of the series, in fact, is about alternate Gallifreys in the Axis.
Also what is stopping the Time Lords from inserting a paradox that go against the "laws of time". If they do that, everything from every point of time happens all at once and then time stops.
TARDIS can exist outside the universe, create paradoxes, freeze an entire civilization in a single moment of time, recreate the universe, allow access to Time Vortex(which is probably a Tipler cylinder). One can already imagine what Time Lords at the height of their power can achieve using their advanced Gallifreyan tech.
Doctor's just one wandering Time Lord who on his own saves people from planetary to universal level threats. He also "rebooted" the whole universe, with prep of course(considering the time needed for prep shouldn't be a problem for Time Lords as they, you know, manipulate time and space to their own will).
It used to be easy. When the Time Lords kept their eye on everything, you could hop between realities, home in time for tea. Then they died, and took it all with them. The walls of reality closed, the worlds were sealed. Everything became that bit less kind.
- Rise of the Cybermen-
The TL's (when around) had full control to manipulate the universe and different dimensions as they seen fit.