I have been reading about the Eastin-Knill theorem, which states that no quantum error correction code can can transversely implement a universal gate set. In this context, for example, the surface code admits Clifford gates in a transversally, which do not form a universal gate set. A universal gate set can be Clifford+T, which is why usually the fault-tolerant T gate over a surface code can be implemented by means of magic state injection. This process requires to distill magic states with sufficiently good quality for being injected in the surface code logical qubit. This also presents some other requirements such as real-time decoding.
However, I have been reading about other possible ways of circumventing the problems that the Eastin-Knill theorem poses for executing arbitrary algorithms over QECs. This is were I crossed the term Shor's fault-tolerant Toffoli gate. However, I am a bit lost about how does this work. As far as I know the H+Toffoli set is universal and, thus, a code should not be able to admit both. Thus I do not see how this gate can circumvent Steane-Knill.