In Batman: Arkham Knight, when you first fight the Arkham Knight he is in the Cloudburst tank, but when you fight Deathstroke it is the same as the Cloudburst fight is.
Where would Deathstroke get the same model?
The tank is a reused asset and (as you mentioned) the whole encounter is essentially the same.
I guess nobody is able to tell the absolute truth behind this, but I simply guess they just ran out of time.
As far as I'm aware there is no real in-lore explanation for this, especially considering it didn't sound typical for Deathstroke (as far as I know the character).
In theory, he could just use the same make of tank, but why the exact same encounter once again?
Besides that, I never really understood where or how they could fit the Cloudburst on the first tank, except using supervillain shenanigans.
Simplest in-universe explanation is that it's just an extra tank that the militia had. Deathstroke apparently had a deal with the Arkham Knight and/or Scarecrow to take over leadership should anything happen to the Arkham Knight, so he would have had access to whatever equipment the militia had. Since Deathstroke would have known that Batman was actively using his Batmobile, he could have used the tank out of a desire to have an advantage over Batman.
I feel that the whole Deathstroke thing is just a Rocksteady "bonus" that people took the wrong way. After the Arkham Knight is unmasked, he no longer leads the militia. So, the developers needed to have someone else lead it for the remaining elective militia battles (to talk over the PA system, issue orders, etc.). They could have had a generic second-in-command and no boss battle, and I think people would have been fine with it. Especially since that the remaining fights against the militia don't advance the story in any way.
Rocksteady probably didn't want to do something that lazy/generic and decided to make it Deathstroke. But they were still being lazy, because 1) they re-used the Deathstroke skin from Arkham Origins [BTW -- couldn't they have at least removed his mask when he's in jail??] and 2) re-used the Cloudburst tank for the boss battle, as you mentioned. The whole thing took very little work on their part. Rocksteady probably thought, "better than nothing, right?" But fans reacted so badly, that it would have been better for Rocksteady to have gone with the generic second-in-command option.
Since Rocksteady was re-using stuff, they might as well have re-used the Deathstroke fight from Origins.