It seems to me that inequality is not particularly useful for eigenstates of A, because isn't it true that we still expect sigma(A)*sigma(B) to obey a similar inequality? Thus, the second term on the LHS of the inequality is already superceded by the relation I'm referring to if you are treating an eigenstate of A, because then surely epsilon(A) will be much larger than sigma(A) (as the latter is essentially zero). So we already know that inequality holds if the system is in an eigenstate of A, as it is not close to the "=" version of the inequality.
As to your initial statement, I don't think anything is wrong with it as written. You can indeed always imagine a measurement with epsilon(A)=0, and then a subsequent one with epsilon(B)=0. That latter quantity does not even appear in either version of the HUP, it's not relevant, it depends on the instrument not the state. In other words, I don't think eta(B) plays any role in epsilon(A) or epsilon(B), nor do the latter combine in any uncertainty relation. But you already know you cannot have sigma(A)*sigma(B) violate the HUP, if A and B are complementary, so disturbances don't enter into that issue. In other words, if you do an accurate preparation in an eigenstate of A, it doesn't matter how many times you measure it, you won't disturb it, and you can do an arbitrarily accurate (noiseless) measurement of B, but you still can't predict what you'll get to any decent precision, because of the HUP.
It seems to me the importance of this new inequality is rather esoteric, in fact. It does seem to give a valid violation of the Heisenberg noise-disturbance relation, by first justifying that it is possible (with the inequality you give), and then by constructing a case that does indeed violate it. But the case it constructs is not an eigenstate of either A or B, so it's not clear what importance that has. If you start with an eigenstate of B (not A), the inequality gets very interesting, because then sigma(B)=0, and the inequality says [epsilon(A)+sigma(A)]*eta(B) obeys the HUP, which means that sigma(A) gets added to epsilon(A) in Heisenberg's own noise-disturbance relation. In that situation, it's not a noise-disturbance relation, it's a noiseplusuncertainty-disturbance relation. That means that when you do very noiseless measurements of A on an eigenstate of B, you do not necessarily need to mess up the B eigenstate much, because the large sigma(A) will insure eta(B) need not be any larger than sigma(B). In principle, you could imagine preparing the state to be extremely close to an eigenstate of B, and you could in principle get essentially zero eta(B), even if you do a noiseless measurement of A, without violating the inequality, which would be of seismic importance if you could really get a low eta(B). However, his analysis does not tell you that you will actually get a result close to the "=" value in that case, and if you get a result much larger than that, it really doesn't do anything useful! In other words, just because you don't necessarily violate the inequality if you use an eigenstate of B, it doesn't necessarily imply you will achieve a low eta(B) with a large sigma(A) and a zero epsilon(A). He doesn't explore in general when you get the all-important =, so necessary if you want to do things like detect gravitational waves, he only quantifies what you get in a case that shows you can violate the Heisenberg version, not a case that actually makes epsilon(A), eta(B), and sigma(B) all low. Only the latter ends up violating the spirit of the HUP, and help us find gravitational waves.