My only problem, was that it wasnt made clear canon that the ENTIRE SERIES was Rikers own personalized version of the Hologram, that he ran in the Holodeck while awaiting trial for the Pegasus incident, in order to prepare his defense by studying Archers first missions and hirs crew.
This would have smoothed out any problems, by leaving question as to whether the events of the series were actual canon history, or it was Rikers modifications for his own purposes and eccentricity.
For example, we know that Worf wouldnt discuss why some Klingons looked different during the TOS era, so Riker could have made up his own hypothesis about it, And likewise he made Data into a successor of Khan Singhs genetic experiments, etc... and even named Archers first ship Enterprise.
(And of course, the inappropriate kinky stuff.... including a burlesque female Vulcan officer...would be pure Riker, along with his possible dislike of Vulcans.
It also would make sense why they never showed the face of Chef, who was played by Richard Sarstedt, and who was also the body double stand in for John Frakes... since they looked alike except for the face, with Frakes only playing Chef in the finale. The implication here, is that was Riker for the whole series, and that was the final surprise ending.
So this seems to be left purposely ambiguous, like the ending of Total Recall.... i.e. it is fairly obvious to geeks like me that it was a simulation, but never officially confirmed.
Timeline for "while awaiting trial" doesn't or shouldn't line up.
TATV perspective:
RIKER: First Officer's Personal Log, Stardate 47457.1. With the
unexpected arrival of Admiral Pressman, my old CO, I find myself in
an awkward position. Counsellor Troi has suggested I might get a few
insights by calling up an historic holo-programme.
The Pegasus perspective:
PICARD: Captain's log, stardate 47457.1. We have been trapped inside the
asteroid for over eight hours. Mister Data and Commander La Forge
inform me that they are nearly ready to engage the cloak.
So canon is these events run simultaneously. Meaning, while the NCC-1701-D is looking for an asteroid, Riker is on the holodeck trying to decide who to betray if it comes to a head. An admiral who's broken treaties but can unravel Riker's past while destroying his future or the lower ranking captain who's doing the morally correct thing and may or may not support him. I've always seen it as the end of TATV is when Riker comes to the conclusion in The Pegasus to say,
RIKER: It means that I can't put this off any longer. Right up until
this moment I had the luxury of time, but now I've got to make a
choice. And, Admiral, I'm afraid my choice is this. I can't let you
start these experiments again. It was wrong twelve years ago, and it
is wrong today.
But he also says this,
RIKER: I've had twelve years to think about it, and if I had it to
do over again I would have grabbed the phaser and pointed it at you
instead of them.
which means the holodeck experience, thus possibly ENT but definitely TATV, was all a waste of time. That's why the episode was a spit in the face for people that watched 4 years, not a Valentines. Riker had already concluded sometime over the previous 12 years that he'd done the wrong thing, but never rang an alarm bell because doing so would have incriminated him as well. And probably Thomas.
The TNG episodes go back in time for the first two following The Pegasus (Homeward and Sub Rosa both occur on Stardate: 47423.9, 12 days before 47457.1, and yes, that's contradictory sloppiness) then jump ahead 40 days or 6-7 weeks for Lower Decks (Stardate: 47566.7). So any trial/court martial that we never saw may have happened during that and is never spoken of again.