Edit: The answer to both of your questions is "no".
The counterexamples below all carry a similar flavor.
Counterexample to the topological version of the first question. (Taking the $C^*$-algebra of continuous $\mathbb{C}$-valued functions on the counterexample gives a counterexample to the $C^*$-algebra version.)
Let $X$ be the following subset of $\mathbb{R}$ with the subspace topology:
$$
X=\{-2,0,2\}\cup\{2-\frac{1}{n}\,|\,n\in\mathbb{N}\}\cup\{-2+\frac{1}{n}\,|\,n\in\mathbb{N}\}.
$$
There is a homeomorphism $F:X\to X$ fixing $-2$ and $2$ and taking each $x\in X-\{\pm 2\}$ to $\min (X\cap (x,2])$ (i.e. the closest point on the right).
Let $B=\{2-\frac{1}{n}\,|\,n=1,2,\dots\}\cup\{2\}$ and $C=\{-2+\frac{1}{n}\,|\,n=1,2,\dots\}\cup\{-2\}$ and write $G=F^{-1}$.
Then
$F(B)=\{2-\frac{1}{n}\,|\,n=2,3,\dots\}\cup\{2\}$ and $G(C)=\{-2+\frac{1}{n}\,|\,n=2,3,\dots\}\cup\{-2\}$
are disjoint, but there is no homeomorphism $H:X\to X$ taking $B$ to $F(B)$ and $C$ to $G(C)$. Indeed, if $H$ existed, then it would restrict to a bijection between $X-B-C=\{0\}$ and $X-F(B)-G(C)=\{-1,0,1\}$, which is absurd.
Counterexample to the the second question and the $C^*$-algebra version of the first question.
Take $A$ to be the abstract ring $\mathbb{C}^{\mathbb{Z}}$. Alternatively, take the subring of $\mathbb{C}^{\mathbb{Z}}$ consisting of sequences $(a_n)_{n\in \mathbb{Z}}$ so that both $\lim_{n\to \infty }a_n$ and $\lim_{n\to -\infty}a_n$ exist --- this is a $C^*$-algebra which is isomorphic to $C(X)$ with $X$ as above.
Let $e_s$ denote the sequence $(a_n)_{n\in \mathbb{Z}}$ for which $a_n=0$ if $n<s$ and $a_n=1$ if $n\geq s$, and let $f_s=1_A-e_s$.
It is easy to see that there are automorphisms of $A$ carrying $e_0$ to $e_1$ and $f_0$ to $f_{-1}$. However, there is not automorphism of $A$ carrying $e_0$ to $e_1$ and $f_0$ to $f_{-1}$ because $e_0+f_0=1_A$ while $e_1+f_{-1}\neq 1_A$.
Furthermore, there is no automorphism of $\mathrm{M}_2(A)$ taking $e_0\oplus f_0$ to $e_1\oplus f_{-1}$, because $\mathrm{Ann}_{\mathrm{Cent}(\mathrm{M}_2(A))}(e_0\oplus f_0)=0$ while $\mathrm{Ann}_{\mathrm{Cent}(\mathrm{M}_2(A))}(e_1\oplus f_{-1})$ is nonzero.