The key sentences from that paper: "If applications and libraries are written in such a manner that the code path and sequence of memory accesses are oblivious

The key sentences from that paper: "If applications and libraries are written in such a manner that the code path and sequence of memory accesses are oblivious to the data and key being used, then all timing side channels are immediately and trivially closed. [We assume that the hardware used does not exhibit data-dependent instruction timings; without this assumption, it is impossible to offer any such guarantees.]" That is, these earlier timing side channels can be avoided, even in the presence of SMT/HyperThreading, by not doing data-dependent branches or memory accesses, and not using instructions with data-dependent timings. For instance, instead of "x = cond ? a() : b();", do something like "mask = cond - 1; x = a() & ~mask | b() & mask;". That is not the case with MDS: even if you carefully avoid data-dependent branches, memory accesses, and instruction timings, you are still vulnerable. It's really a new vulnerability class.