The result you state follows from the fact that every countable subset of $T_X$ is contained in a 2-generated subsemigroup. See this question for more details:
Evans' theorem of embeddings into 2-generator semigroup.
As for if $T_X\setminus S$ is uncountable, then $\operatorname{rank}(T_X:S)$ is uncountable, this is just plain wrong: $T_X\setminus S_X$ is uncountable but $\operatorname{rank}(T_X:S_X)=2$ where $S_X$ is the symmetric group.
The correct argument goes like this: if there is a countable set that together with $S$ generates $T_X$, then there is a set with at most two elements since every countable set is contained in 2-generated subsemigroup. Hence the relative rank is at most 2 in this case. If there is no countable set that together with $S$ generates $T_X$, then the relative rank is uncountable.