Well, I think I may have an explanation why it has been implemented this way (not that I like it, mind you).
All of BattleMaster's manoeuvres are not augmentations of the basic attack, they are separate attacks, and (at least as of now) we have no ways to somehow augment them. Because of that, their damage comes as a single number.
Contrarywise, the Warlock's EB is augmented by Agonising Blast as soon as we pick this Invocation. However, it's still the same EB as the one we had at level 1. Apparently, implementing a separate EB+AB attack (so that it would have a single number, like manoeuvres) would result in Warlocks having 2 similarly looking EB icons: one basic, and another one which includes AB bonus in it (and this is where, I suspect, engine's limitations come into play). I perfectly understand why Larian decided not to go this way: either we would have 2 identically looking, yet different, EB icons on the hotbar, or they would have to implement a complete replacement of one skill with another. Considering that a lot of Warlock's invocations are essentially EB's augments, the total number of possible permutations will be huge.
Unfortunately, it resulted in this particular side effect, which only starts to matter when your target has damage reduction.
Regarding Rage - did you test the basic attack under the effect of Rage, or the specific attacks (like Reckless Attack, etc)? With the latter, they should be implemented in the same way as BM's manoeuvres, and have a single number. Thanks for the idea, I'll check it as well.
Sneak Attack: I'm not surprised. There are lots of issues with the internal implementation of SA (maybe it was one of the very first things Larian did, when they were just experimenting with how things can be done?). For example, occasionally it goes on
cooldown, although I haven't seen this in Patch 7 yet.
