While regenerating, the Master says that if the Doctor can be young and strong, so can he. This works as Foreshadowing for the revelation at the end of "The Name of the Doctor", that there was an older, as yet unseen regeneration of the Doctor who likewise had grey hair.
It was more likely a reference to the fact that most (but not all) of the Doctors in the classic series were notably older than the Tenth Doctor.
When Yana opens the fobwatch, the Doctor has an Oh, Crap! face. At first this doesn't make sense, however if you stop and think about it... of all the people that fought in the Time War who would have the likeliest chance of surviving? Obviously the Doctor and some of the Daleks, but also THE MASTER!
If you consider that he's recalling the events of Time Crash from when he was the Fifth Doctor (if he can recall it, since he hasn't done it yet), where he learnt that he would be facing the Master again in his future incarnation... The look of horror on his face is his realisation that that moment is now.
"The End of Time" reveals that it wasn't just the Master that the Doctor was fearful of; almost any other one could be a problem.
The Doctor, upon reading what year the console's sensors have registered, protests that it's "impossible" for them to be 100 trillion years in the future. "Hell Bent" suggests that he wasn't just being amazed, but meant it literally: the physical universe, itself, won't last nearly that long. Rather, "100 trillion" was most likely a glitch: a reading that the TARDIS defaults to when she ventures so close to the end of Time that her chronometer can't interpret its readings any more. Which would explain why the Master chose to hide out in such a distant era, despite it being doomed: it's the one temporal destination in which the Time Lords weren't able to navigate properly, so they couldn't track him down and execute him for desertion or drag his sorry arse back into the Time War.
Why is Yana so different from the Master? Could very well be a subtle Shout-Out to the previous story with a fob watch, where John Smith was outright romantic, willing to allow children to be beaten, and obedient to authority-completely the opposite of the Doctor.
As we'll learn later, yes. And as we'll learn with Missy, more yes, but also kind of no.
When the Master regenerates, we see the same sort of glowing energy pour out of him as when other revival-era Time Lords do so, except that there's a sickly green tinge to the usual golden streams of force. This implies that the Master's many years of existing in the stolen bodies of Human Aliens and humans and biologically altering himself, cheating the usual limitation on how many regenerations a Time Lord gets, have permanently corrupted the process in some way, even after the High Council granted him a new series of lives so he could fight in the Time War.
The idea humanity evolved back into their present-day form? Strange but somewhat plausible. Having nearly-identical technology to the 20th and 21st centuries, not so much. But then you realize Yana could have subconsciously built the silo and their vehicles from remnants of the Master's memories. After all, John Smith still seemed to remember Gallifrey, even if it was only the name.
If the Master wanted to escape the Time War because he was afraid, why did he hide right before the universe itself ends? Earlier in the episode the Doctor mentions that 100 trillion is so far into the future that not even the Time Lords have been there. If there's anywhere and when in the universe where he can be guaranteed to be outside the War's reach, it was there and then.
Professor Yana's computer was intended to look like a TARDIS console, only for the writers to nix the idea when they figured the Doctor would notice this. And yet, in his next incarnation, the Doctor failed to realise he was standing around several hundred TARDIS corpses. Which means the Master could in all likelihood have had a TARDIS with him when he fled to the year one trillion, and later on took it to pieces without even realising what it was.
