[guided]The characteristic polynomial of $L(M)$ is defined by summing the Möbius function over flats:
\begin{align*}
\chi_{L(M)}(t)=\sum_{F\in L(M)}\mu_{L(M)}(\varnothing,F)t^{r-\rho(F)}.
\end{align*}
To rewrite this as a sum over all subsets of $E$, we group subsets according to their closure. Define the map
\begin{align*}
S:L(M)&\to \mathbb Z
\end{align*}
\begin{align*}
F&\mapsto \sum_{\substack{A\subset E, \operatorname{cl}_M(A)=F}}(-1)^{|A|}.
\end{align*}
We want to prove that $S(F)$ is exactly $\mu_{L(M)}(\varnothing,F)$.
Fix a flat $F$. A subset $A\subset E$ has closure contained in $F$ if and only if $A\subset F$, because $F$ is closed. Therefore, summing $S(G)$ over all flats $G\subset F$ counts every subset $A\subset F$ exactly once, namely under the flat $G=\operatorname{cl}_M(A)$. Thus
\begin{align*}
\sum_{\substack{G\in L(M), G\subset F}}S(G)=\sum_{A\subset F}(-1)^{|A|}.
\end{align*}
The last sum is the binomial expansion of $(1-1)^{|F|}$. It equals $1$ when $F=\varnothing$ and equals $0$ when $F\ne\varnothing$.
Because $M$ is loopless, $\operatorname{cl}_M(\varnothing)=\varnothing$, so $\varnothing$ is the minimum flat. The defining recursion for the Möbius function on the finite poset $L(M)$, equivalently [citetheorem:8094] applied to the interval from $\varnothing$ to $F$, says that the unique function $F\mapsto \mu_{L(M)}(\varnothing,F)$ satisfies
\begin{align*}
\sum_{\substack{G\in L(M), G\subset F}}\mu_{L(M)}(\varnothing,G)=1
\end{align*}
when $F=\varnothing$, and satisfies
\begin{align*}
\sum_{\substack{G\in L(M), G\subset F}}\mu_{L(M)}(\varnothing,G)=0
\end{align*}
when $F\ne\varnothing$. The function $S$ satisfies the same equations, hence $S(F)=\mu_{L(M)}(\varnothing,F)$ for every flat $F$.
Finally, rank is unchanged by closure, so $\rho(A)=\rho(\operatorname{cl}_M(A))$. Substituting the identity for $S(F)$ into the characteristic polynomial gives
\begin{align*}
\chi_{L(M)}(t)=\sum_{F\in L(M)}\mu_{L(M)}(\varnothing,F)t^{r-\rho(F)}=\sum_{A\subset E}(-1)^{|A|}t^{r-\rho(A)}.
\end{align*}[/guided]