Yeah, Tolwyn in Wing Commander II is a little more complex: he and Blair certainly hate each other (he blames Blair for the loss of the Tiger's Claw, Blair blames him for cashiering him). But the story shows us that it's specifically their relationship, not an indicator that one is good and the other is evil. There are multiple times where Blair tries to complain about what a hardass Tolwyn is (to Sparks, to Angel, etc.) and he's coincidentally shot down because to those characters Tolwyn is the fighting Admiral who has been leading them. I was just talking about this in an unrelated Twitter thread but the game's original script outline has a stronger end for Tolwyn where he punches out a reporter who is denigrating the war effort. This is all followed logically in the Special Operations disks which have a much rosier relationship between Tolwyn and Blair, post Jazz… and this was where, creatively, the novels spun off from the games, with Dr. Forstchen writing from the status quo as of Special Operations 1: Blair and Tolwyn are friends, Bear is a cool new hero, etc.
Wing Commander III gets some shit for casting generic bad guy Malcolm McDowell as Tolwyn, with folks saying it's inevitable that he was going to become a villain instead of an antagonist… but I do think the game actually treats Tolwyn okay. We specifically have a line referencing the end of WC2 when he arrives at Torgo: "I thought at long last we’d achieved a measure of respect for each other. Obviously I was wrong."
And the conflict in WC3 isn't too hard to figure out: Blair blames Tolwyn for Angel's disappearance ("she's on some damn covert op for Tolwyn") and for reassigning him to a second ringer carrier (she's no Concordia!) after a tour as Wing Commander on his flagship! Tolwyn, on the other hand, doesn't see either of these things: he knows he didn't actually send Angel to her death (Paladin did!) and he moved Blair to the Victory /specifically because he wanted his best pilot to protect the Behemoth./ And Blair does EXACTLY THE SAME THING as he did in WC2: he bitches to anybody who will listen about Tolwyn… except on the Victory there's no one to defend him, just a lot of people unhappy that he's sidelined Captain Eisen. And people read the ending wrong too: the idea isn't that Tolwyn was crazy to make the Behemoth… it ends up being exactly the same thing Blair has to do, destroy Kilrah and kill a zillion civilians in the process of ending the war. It's not a coincidence that Tolwyn comes back to active service to sign the surrender at the end!
Wing Commander IV obviously makes Tolwyn a crazy person (either ruined by war or by being Malcolm McDowell) but the relationship is still pretty complex before Blair knows that. Tolwyn is obviously unhappy that Blair, his man, is the face of the great victory over the Kilrathi… and Blair isn't happy to be called back to active service to hunt pirates (even though again, this is Tolwyn's plan within a plan and thinking he's rewarding his loyal officer; he thinks Blair will support his ideology and wants him to be part of what's coming). Part of that is also how fans lens these sorts of things… while the Special Operations stories (and the novels) are HUGE for us, they weren't really particularly special to the folks /making/ the later games. The mission disks were made with small, inexperienced teams in a matter of a few weeks while most of the development team moved on to the next game.
Wing Commander Academy adds some context, with the idea that Blair is morally opposed to Tolwyn because Tolwyn is willing to throw away lives to win the war (the intent being to prelude to the fact that Blair will someday have to make those exact same decisions). It also introduces the idea, furthered in the movie tie-in material, that Tolwyn was particularly influential in Blair's early career, with Tolwyn having served with Blair's father and making sure Chris got special treatment at the Academy and in his early assignment to the Tiger's Claw (none of which Blair appreciates).
To me though, I still don't think Blair ever *truly* forgave Tolwyn for the Engima Incident. Since everything after that, Blair would now always have doubts on how Tolwyn handles different situations. It didn't help that Tolwyn basically forced Eisen out of command for a few missions. And he was so goal oriented, he didn't bother to do security checks for Hobbes leaking data. (This is also a plot hole/convenience with Royln though that always made me angry).
1. Tolwyn easily dismissed probably one the best, by the book, pilots in Confed. Him destroying a carrier, especially one he served on for so long, would make no sense.
2. Tolwyn single handedly caused Blair's name to be tarnished, and used Blair as a propaganda piece against the Kilrathi. "See look what the Kilrathi do to our pilots!"
3. Blair had to literally fight his way back up to dismiss the "Coward of K'Thrag Mag" title. And people being the way they are, could see some "truth" in that.
4. Blair is so loyal, even though people hated him he risked his life, and disobeyed orders several times in WC2 to save lives.
5. Any normal pilots Morale would be shot dealing with that, but Blair fought through that. (hence why I thought the "Heart of the Tiger" title was a genius move in the script. (I mean look at Dallas in WCP, he was scared even firing shots).
6. Even the negligence charge makes no sense, a surprise attack can go every which way in the situation.
To me it's just plain idiocy, that in the instances where he fought the stealth fighters, in every instance his flight recorder was damaged. Take a camera FFS. Any amateur detective can know, especially as someone as smart as Tolwyn, would say "okay I think something is up here."
Coupled with everything else you said, Blair will always have doubts in Tolwyn's decision making abilities after the Enigma Incident. This was further cemented when Tolwyn had obvious jealously for Blair delivering the killing blow to Kilrah.
Personally, if I worked my ass off as Blair did, and was a by the book pilot, and I got screwed because of an incident and something I didn't do, I could never forgive that person, for almost destroying my life as a pilot, and as a person. It makes it worse, since Tolwyn is an Admiral, and you have no choice to follow orders, so Blair was backed into a corner. If it wasn't for Jazz's slip up, Blair would have been screwed.