complexity theory – A question about domains in Karp reductions

A basic question or request for clarification regarding Karp reducibility:

Let $Sigma^*$ be the set of all finite strings of 0’s and 1’s. Call a subset of $Sigma^*$ a language. Let $Pi$ denote the set of all functions from $Sigma^*$ into $Sigma^*$ that are computable in polynomial time. According to Karp, a language $L$ is reducible to a language $M$, also denoted $L leq_K M$, if there is a function $f in Pi$ such that $f(x) in M Leftrightarrow x in L$.

For many problems, however, we are interested in the difficulty of determining membership in subsets of domains other than $Sigma^*$. To address this, Karp briefly discusses encodings: Given a domain $D$, there is often a natural “one-one” encoding, $e: D rightarrow Sigma^*$. He then says that given a set $T subset D$, $T$ is recognizable in polynomial time if $e(T) in mathcal{P}$. But don’t we, in practice, typically consider $T$ to be recognizable in polynomial time if, for any $x in D$, we can determine whether $x in T$ in polynomial time? On the face of it, this doesn’t seem to be the same as Karp’s definition, since there is no guarantee that $e(D) = Sigma^*$.

Similarly, according to Karp, $T leq_K U$ where $T subset D$ and $U subset D’$ if $e(T) leq_K e'(U)$ where $e: D rightarrow Sigma^*$ and $e’: D’ rightarrow Sigma^*$. However, when we are actually proving $T leq_K U$ for some real $T$, $U$, $D$, and $D’$, don’t we frequently just define an $f: D rightarrow D’$ computable in polynomial time, confirm that $f(x) in D’$ for any $x in D$, and show that $f(x) in U Leftrightarrow x in T$ for any $x in D$? Again, this doesn’t seem to be the same thing as Karp’s definition if $e(D) neq Sigma^*$.

What am I missing?