Your question is unprecise. Yous state that you have a problem
understanding some parts of the text, but without any further hint as to the nature of the problem.
You should be more specific about what is bothering you in this
construction of the DFA $D$. For example, what do you think is wrong
with the start state of $D$ being the set $\{1,3\}$. Is it the fact
that it is a set of states, or the fact that it is this specific set
of states $\{1,3\}$?
I suspect it may be the former, so I will try to answer that. I do not
have Sipser's book, so that I cannot relate specifically to his
presentation, other than with the page you give.
The major point in this is that state names do not matter. In the
example, the names of the initial NFA $N_4$ are the integers $1$, $2$ and
$3$. Now, you might wonder whether it is actually the first three
natural integers, or only the three characters that represent them (or even, possibly, three strings of one character each). The
fact is that it is irrelevant, that it does not matter. All you really need
to describe/define your automaton is to have 3 distinct states, and to
be able to distinguish them in some way so that you can tell where you
start, how you can pass from one to another on some input, and which
is accepting.
As usual, when you talk about something, the best way is to identify
it with a name, which should refer to it only in a given context. It
can be "babou" right now if I am the something. It can be the
character "3" or the string "III" if it is the third natural integer,
though you can also call it "third natural interger" which people will
understand, or it can be the name "Joe" if you have first given the
notational definition:
Let Joe be a name for the third natural integer.
or more accurately
Let "Joe" be a name for the third natural integer.
Though the quotes are needed only in the definition, since the
beginning of this definition is about the name, rather than what is
being named, quotes are not to be used when the name stands for what
is being named. The name of Mary is "Mary", and "dogs" never bites
(the "s" ending "bites" is intentional) while dogs may bite.
You can play a lot with names, which is sometimes very convenient. In
particular, there is no reasons that names should be only spoken
utterances, or written character strings. It works as well if you take
names from any set, such as integers, or sets of integers for example.
Since other things, such as integers or sets of integers, need to be
named too to talk about them, it is hard to know whether you are using
themselves or their names when the names is written down. We have seen
that there are notational devices to make the distinction when it is
important (using quotes, for example), but you can often forget about
it.
So here $1$, $2$, and $3$ are the names of the states. We now see that
whether they stand for the character or the integer does not actually
matter muuch.
If you take a DFA and change consistently the name of a state of the
initial NFA $N_4$, but you might describe the same NFA with the names
$9$, $8$, and $7$, or with $26$, $3$ and $15$, or with $1$, $2$ and
$3$ assigned differently to the states so that the start state would
now be $2$ (in the picture, you move $1$, $2$ and $3$, but you do not
touch the start arrow or any other part of the picture), or it could even be the names Huey, Dewey,
and Louie, or the names "foo", $2$ and "blue" (which is very useful if you describe the NFA with a poem).
In other words, in languages and automata theory, when you talk of a
set of states or symbols, you can take any set of mathematical objects
that you can enumerate (give me some time to think about sets that are countable but not recursively enumerable ... but this is no worry of yours). They do not even need to come from a
consistent source. You only want them as names in order to describe
and run you automaton.
But this should not encourage you to use strange naming. This naming
freedom should rather be used to make things easier to understand and
remember. This is probably why Sipser used $1$ for the start state.
You have exactly the same situation in programming, when you have to
choose names/identifiers for variables, functions, classes or other
entities, though these names are usually restricted to alphanumeric
strings. Good programming practice recommands the use of identifiers
that are meaningful, and help understand the program.
When building the DFA $D$, you can use any name you want for the
states of $D$. However, it is convenient to use sets of names
used for the states of the NFA $N_4$. This is usually simplified into saying that
each state of $D$ is a subset of the states of $N_4$.
This choice of names is convenient, and helps understanding, because
because a state of $D$ is intended to mimic (in some precise sense) the behavior of
several states of $N_4$, precisely those it contains.
A complementary or alternative view of this is to consider that
automata that use different state names are defined up to a renaming
of states. What one is interested in is the equivalence class up to
a renaming equivalence relation, since renaming does not change the
behavior of the automaton.
Understanding the use of names is not as obvious as it may seem, and
it can raise sometimes thornier technical issues, though not really
here.
See for example:
E(R) = {q| q can be reached from R by traveling along 0 or more " arrows}.
$\endgroup$