Do the proofs that permanent is not in uniform $\mathsf{TC^0}$ relativize?
Any separation of classes closed under "polynomial resources" has an oracle making them equal. (This is provided the oracle mechanism is fair and allows both machine models to make polynomial length queries and no more.)

Let $TC0^{O}$ be "$TC0$ with gates for oracle $O$". Letting $O$ be a $PSPACE$-complete language under $TC0$ reductions, we have $TC0^{O} = PSPACE = PSPACE^{O} = PP^{O}$, where  in the oracle mechanism for $PSPACE$, we count the space usage of the oracle tape along with the rest of the memory. (So only polynomially length queries are asked.) Such an equality holds for many classes "closed under polynomial resources", in the sense that they can ask polynomially length queries to an oracle, but no larger. These classes include stuff like $AC0$, $TC0$, $LOGSPACE$ (under a different oracle mechanism which does not count oracle queries towards the space bound), $P$, $NP$, $PH$, and $PP$. So any separation of classes in this list must necessarily use some kind of "non-relativizing" argument. This also implies (for example) that the natural proofs of things like Parity not in $AC0$ are non-relativizing (but this is even easier: all you need here is an oracle for parity, so you get $AC0[2]$).

In the collection of proofs you cite, I believe most of them (if not all) work by assuming $TC0 = PP$ and deriving a contradiction. These kinds of results are called "indirect diagonalization". So a relativization of their proof would have to say: "if $TC0^{O} = PP^{O}$, then contradiction..." but this assumption is actually true for some oracles $O$.

In the comments, it was pointed out that $LOGSPACE^{O} = PSPACE^{O}$ in the way that I am using it. These are just subtleties with the oracle mechanism. On the LOGSPACE side, the query tape cannot be part of the space bound, since queries are polynomial length. On the PSPACE side, the query tape is taken as part of the space bound. That was to make things "fair". But if you give them exactly the same oracle mechanism then indeed you can separate them again by diagonalization. For instance, if queries do not count towards the space bound, then in PSPACE^{PSPACE} you can ask exponentially long questions to PSPACE, so this in fact contains EXPSPACE. I apologize for not saying this explicitly earlier. 

Space-bounded computation is very subtle with respect to oracles. See page 5 of this article by Fortnow for a good summary of why oracle and space-bounded computation don't always mix.