Which is probably why it’s called “The Time of The Doctor.”
But, yes…everything that happens in seasons 5 to 7 essentially happened during the time frame covered by that one special…as much as that can be said where time travel is concerned.
But, consider this, Madame Kovarian’s branch of the church does not split off until after Tasha Lem declares that “silence will fall.” At some point after they split off, they go back in time and cause The Doctor’s TARDIS to explode, creating the cracks in time. We first encounter the cracks in The Eleventh Hour, so, from a certain point of view, the beginning of The Time of The Doctor happens before that. So, in a way, throughout the whole of his incarnation as the Eleventh Doctor, the Doctor was also on Trenzalore.
In fact, the only part of it that happens outside of the timescale of The Time of The Doctor is The Name of The Doctor, but the events on Trenzalore there no longer happened due to the wild card that was the intervention of Clara which fundamentally altered The Doctor’s time line…she saved him throughout his own time line, including at Trenzalore where she convinced the Time Lords to save him.
Of course, The Doctor, Clara and those involved still remember those events, because they happened to them, but as time travellers they exist apart from time, to a certain extent…so although those events will never happen, they did happen for those who lived through them. See? Simple.
The Eleventh’s run has all been about stories…it’s a story within a story. It’s also been all about effects with no cause…and ultimately ALL of the events of season five to seven have been caused by the fact that he didn’t destroy Gallifrey but, instead, saved it, leaving it stranded somewhere outside the universe…something that didn’t happen until the second to last story.
Eleven’s story needs to be seen as a whole…because nothing can make sense outside of the context of The Doctor’s decision to save Gallifrey. For three seasons he suffered from the effects of a choice he didn’t even know he’d made…while carrying the guilt…the effects…of something he hadn’t done.
As I said, it’s all been about cause and effect…effects with no cause…
Bloody marvellous if you ask me.