In both canons, the absence of the Empire’s civilian government in stories set after ROTJ. Assassinating a head of state doesn’t cause the civilian government to spontaneously be replaced by a military junta.
Well, Palpatine got rid of the imperial senate during the events of ANH and gave power to all of the Moffs (regional governors), who were the ones who started fighting each other after ROTJ.
Thrawn was an Admiral, not a Moff.
Yes, but the post-Endor EU stories consists of so much more than just Thrawn.
Many of the feuding warlords, like f.ex. Ardus Kaine, were Moffs. Also, the term “warlord” in Legends was basically a military/governor combination, presumably so that it would make sense continuity-wise while also justifying the antagonists to be military leaders.
I get what you’re saying about how an Imperial civilian government outside the military would make sense, but ANH established that Palpatine handed political power over to the governors, who were more or less parts of the military anyway, and the EU even had characters like Ysanne Isard and Sate Pestage, who were both politicians and who both ruled the empire for a while. Pestage basically got the role the same way a vice-president might take over after a presidential assassination. The military didn’t spontaneously take over the empire in the EU, but power-hungry moffs and admirals started undermining and assassinating each other, and all the in-fighting made it easier for the Rebels to take over Coruscant and the core-worlds. The moffs and warlords then held on to their territories and fought the New Republic as well as each other for several years until eventually being unified (forcefully of course) by Natasi Daala who eventually handed over the Imperial Remnant to Gilad Pellaeon, who in turn made a treaty with the New Republic some 10 years after Endor.
And if you wish to dabble in Dark Empire territory then you could assume that this was all some grand plan by Palpatine to weed out the traitors from the loyalists, etc, etc. Though even the EU people tended to ignore this as much as possible, at least pre-ROTS, as it makes everything very convoluted.
Overall though, the larger narrative of the EU (though admittedly a fair amount of this came in the form of retcons) does make sense overall. At least in Legends the Empire didn’t just collapse in a single year after the death of Palpatine like it does in canon (though the Mandalorian seems to have retconned it somewhat).
PS. EckhartsLadder made a very succinct video summarizing the most important post-Endor factions/warlords; https://www.youtube.com/watch?v=lmz7Jon7gTY