What is true more precisely is that we have an additive error bound
$$\left( 1 + \frac{1}{n} \right)^n = e + O \left( \frac{1}{n} \right)$$
and the form of the additive error is important. In this problem you need to multiply by $\frac{n}{e}$ and doing so gives
$$\frac{n}{e} \left( 1 + \frac{1}{n} \right)^n = n + O(1)$$
meaning this approximation now incurs some bounded additive error, which means it cannot be used to determine the value of the limit $S_2$ (although it does correctly suggest that the limit exists). The limit of the ratios is not enough information to determine whether or not this will happen in a given situation. To compute $S_2$ correctly you need to know the next term in the asymptotic expansion (in fact determining $S_2$ is equivalent to determining the next term in the asymptotic expansion), which turns out to be
$$\left( 1 + \frac{1}{n} \right)^n = e - \frac{e}{2n} + O \left( \frac{1}{n^2} \right).$$
In the first situation $S_1$ can be computed by using Stirling's approximation to get an additive error bound of the form
$$\sqrt[n]{n!} = \frac{n}{e} + \frac{\log 2 \pi n}{2e} + o(1)$$
which will give $S_1 = \frac{1}{e}$. For computing this limit you can basically ignore additive error of the size any function $f(n)$ such that $\lim_{n \to \infty} f(n+1) - f(n) = 0$, which basically means any function growing sublinearly. So more or less the dominant part $\left( \frac{n}{e} \right)^n$ of Stirling's approximation is enough, but you got a little lucky.
So in general it just depends on what is happening to the function. Potentially the entire asymptotic expansion may be necessary, because the limit you're trying to evaluate may e.g. subtract the first $k$ terms in the asymptotic expansion and then require the $k+1$-th term. For example, if a problem asked you to evaluate the limit
$$\lim_{n \to \infty} n^2 \left( \left( 1 + \frac{1}{n} \right)^n - e + \frac{e}{2n} \right)$$
that's equivalent to asking for the quadratic term in the asymptotic expansion, which turns out to be $\frac{11e}{24n^2}$.
A comment on how to find the asymptotic expansion of $f(n) = \left( 1 + \frac{1}{n} \right)^n$. It would in principle be possible to do this using the binomial theorem but I think it gets pretty messy and annoying. We can do it more easily by taking the logarithm to get
$$\log f(n) = n \log \left( 1 + \frac{1}{n} \right) = \sum_{k=0}^{\infty} (-1)^{k-1} \frac{x^k}{k+1} = 1 - \frac{1}{2n} + \frac{1}{3n^2} \mp \dots $$
which can be exponentiated term-by-term, e.g. in WolframAlpha. For example the cubic term is given by expanding
$$f(n) = \exp \left( 1 - \frac{1}{2n} + \frac{1}{3n^2} - \frac{1}{4n^3} \pm \dots \right) = e - \frac{e}{2n} + \frac{11e}{24n^2} - \frac{7e}{16n^3} \pm \dots.$$