An interesting, if disturbing update. Though it was nice to see "На нож!" appearing earlier than in OTL
Also nice to see the war turning in Bulgaria's favor, though the way it's going the Austrians may well attempt to replace the Ottomans.
Indeed, I decided it fits well here. It will certainly return again and again for sure. As for the Austrians, they probably won't try to occupy as Bulgaria is too far from their own centers. But occupation is not the only type of domination.
Considering the behavior of the rebels against the Turkish population, I can well understand why it would happen, though I have some doubts whether it would be to this extent. While in OTL there were attacks upon the Muslim population in Thrace and many fled, there wasn't the near destruction of the Muslim presence in Thrace as has happened in your scenario. In fact many of those had fled returned after the peace was signed so there were over 200 thousand Muslims in Eastern Rumelia, nearly as many as before the war. Of course I understand that here the Bulgarian army is much bigger than the small volunteer corps fighting under the Russians and there are far more recent atrocities that were committed against the Bulgarians, so this is a factor here. And I agree that Berkovski would be unlikely to attempt to rein them in. Still, I'm not entirely sure how realistic this course of events would be, especially considering the traditional relations between Bulgarians and the Muslim minorities in OTL, where the option of mass removal of the Muslim population has never been the dominant opinion (of course I'm well aware that unavoidable bias on my part is probably influencing my thinking). But it's your timeline and it's far from finished, so I'm not rushing to judgment yet.
All of those points are absolutely valid, the reason for the atrocities TTL happened as opposite to OTL are varied, and you touched upon some of them. First of all the timing is very crucial, thanks to the horrid events at Sofia and the very recent much much more bloody events at Shipka it is safe to assume that the Rebels, which are now pretty much an active army, will be itching for a response. Of course, the relations between Bulgarians and Muslims play a role here as to mitigate a lot of the potential atrocities, because it could have been much worse and the death toll much higher. The other part of it all is where it happened, as I noted in Kazanlak the army didn't touch the local muslim population, but at that point the military was most likely exhausted broken but filled with hope, once that hope was broken by the enormous loss of life and desperation of the Iron Gate before Zagora however, things changed rather quickly. So you have a large mass of angry men, who just came out of one of the most vicious fights in the tight confined spaces of the Iron Gate who are disgruntled, tired and angry, most probably lost relatives to the Turks and their Bashi-bouzuk and would be happy to seek revenge. Add that to the command not willing or able to reign them in as they stream into Stara Zagora you end up with a horrible situation where any resistance is squashed with excessive force and the Muslims are chased out at best and I don't really want to talk about the worst. A lot of this includes the Austrians, this wasn't a solely Bulgarian decision or event, it was most likely triggered by the Austrians who on the other hand have no reservations about "purging" the city. So it was most likely the Austrians who pulled the proverbial genie from the bottle and those Bulgarians who seek revenge were quick to join them.
From that point forward, I should have noted that after Zagora the number of atrocities form Bulgarians upon Muslims declined considerably, with Zagora serving as more an exception rather then the rule, but attrocities still happen afterwords, both by volunteer Bulgarians and mostly by Austrian military.
And of course the arrest of Levski doesn't bode well. Whatever the fighting qualities of Benkovski, he does not seem at all the type to be able to lead a country in peace. And disunion is the last thing needed at this point among the rebels, when the country might be about to become part of the game of Empires.
Oh I am under no illusion, neither is Benkovski, there is a reason why he arrested him so quietly and pulled him to the side. He will be trying to close Levski on the sideline and lie about his arrest rather then face half his military revolting against him. And I absolutely agree that this is the last thing the Bulgarian side needs, but with a lot of strong personalities in this military and considering its size, we can safely assume that a split will happen anyways sooner or later, Benkovski is just delaying the inevitable until after the war.
On other matters, what are the Russian doing? They can't be too happy about Austria-Hungary seemingly taking over Bulgaria when influence was supposed to be shared.
Oh they are unhappy alright and they will make their discontent heard pretty soon.