$\gdef\cal{\mathcal }$ $\gdef\ccal{\mathcal C}$ $\gdef\dcal{\mathcal D}$
Let $\cal C, \dcal$ be pre-triangulated $A_\infty$ (or dg) categories, $F, G: \ccal \to \dcal$ exact $A_\infty$ functors. We assume $\cal C_{gen}$ is a full subcategory of $\cal C$ that generate $\cal C$ in the sense that $Tw(\cal C_{gen}) \cong \cal C$.
It is true that
However, it is not true that $\eta_{gen}$ is determined by $\eta_T: F(T) \to G(T)$ for all $T \in \ccal_{gen}$ that satisfies compatibility conditions with morphisms, i.e. for all $f: T_1 \to T_2$, we have $G(f) \circ \eta_{T_1} = \eta_{T_2} \circ F(f)$ in $Hom(F(T_1), G(T_2))$.
In this note, we give an example of a non-trivial natural transformation $\eta$ of degree $0$, such that $\eta_T = 0$ for all generator $T$.
We work throughout with cohomological grading conventions.
An $A_\infty$ category $\mathcal{C}$ consists of a collection of objects together with graded morphism spaces and higher compositions
$$ m_k : \mathrm{Hom}(X_{k-1},X_k)\otimes \cdots \otimes \mathrm{Hom}(X_0,X_1) \to \mathrm{Hom}(X_0,X_k)[2-k], $$
satisfying the usual $A_\infty$ relations. A dg category is the special case where $m_k=0$ for $k\ge 3$.
An $A_\infty$ functor $F:\mathcal{C}\to\mathcal{D}$ consists of maps
$$ F^k : \mathrm{Hom}(X_{k-1},X_k)\otimes \cdots \otimes \mathrm{Hom}(X_0,X_1) \to \mathrm{Hom}(F(X_0),F(X_k))[1-k], $$
satisfying compatibility equations with the $m_k$'s. When $F^k=0$ for $k\ge 2$, this is just an honest dg functor.
Given two $A_\infty$ functors $F,G:\mathcal{C}\to\mathcal{D}$, an $A_\infty$ natural transformation $\eta:F\Rightarrow G$ of degree $d$ consists of multilinear maps
$$ \eta^k : \mathrm{Hom}(X_{k-1},X_k)\otimes \cdots \otimes \mathrm{Hom}(X_0,X_1) \to \mathrm{Hom}(F(X_0),G(X_k))[d-k], $$
satisfying a hierarchy of equations generalizing the usual naturality condition. In particular:
Let $\ccal_{\mathrm{gen}}$ be a $A_\infty$ category. Its twisted-complex envelope $\mathcal{C} = Tw(C_{\mathrm{gen}})$ is the $A_\infty$ category with objects the twisted complexes $(\oplus_i X_i[d_i], \delta)$.
A basic (and standard) fact is that: any $A_\infty$ functor $F_{gen}:\ccal_{\mathrm{gen}}\to \mathcal{D}$ into a pretriangulated $A_\infty$ category $\mathcal{D}$ extends canonically to an $A_\infty$ functor $${F}:\mathcal{C} \to Tw(\mathcal{D}) \cong \mathcal{D}.$$
$$ (\oplus_i X_i[d_i], \delta) \mapsto (\oplus_i F^0(X_i[d_i]), F^1(\delta) + F^2(\delta,\delta) + \cdots ) $$
The category $C_{\mathrm{gen}}$ has three objects
$$ T_1,\quad T_2,\quad T_3. $$
For each pair $(i,j)$ there is a unique degree $0$ morphism $a_{ij}:T_i\to T_j$, with $a_{ii}=e_i$ the identity. In addition, each object carries a distinguished endomorphism $$t_i:T_i\to T_i.$$
Composition are given by
$$ a_{ij}a_{jk}= \begin{cases} a_{ik} & \text{if } i\le j\le k \text{ or } i\ge j\ge k \cr 0 & \text{ otherwise} \end{cases} $$
$$ \forall i\neq j \quad a_{ji} t_i = t_i a_{ij} = 0, \quad t_i t_i=0. $$
There is no differential on morphisms.
We now define a functor
$$ B : \ccal \to \ccal, $$
which should be thought of as a toy “braiding.”
$$ B(T_1) = T_1,\qquad B(T_3) = T_3, $$
and
$$ B(T_2) = \big[ T_2 \xrightarrow{(a_{21},\,a_{23})} T_1 \oplus T_3 \big], $$
where $T_2$ sits in degree $-1$ and $T_1 \oplus T_3$ in degree $0$.
The composites
$$ T_2 \xrightarrow{a_{21}} T_1 \xrightarrow{a_{12}} T_2,\qquad T_2 \xrightarrow{a_{23}} T_3 \xrightarrow{a_{32}} T_2 $$
are zero in $C_{\mathrm{gen}}$, but their images under $B^1$ are not zero endomorphisms of $B(T_2)$. Therefore, $B$ cannot be a strict dg functor.
We fix this by declaring $B$ to be an $A_\infty$ functor with nonzero $B^2$ on exactly these zig--zag pairs:
A quick way to summarize the needed $A_\infty$ constraint on $A_\infty$ functors between dg cats $B: C \to D$ is the $k=2$ equation:
$$ \mu_D^1(B^2(f_2,f_1)) + \mu_D^2(B^1(f_2), B^1(f_1)) = B^1(\mu_C^2(f_2,f_1)) + B^2(\mu_C^1(f_2),f_1) + (-1)^{|f_2|} B^2(f_2,\mu_C^1(f_1)). $$
A direct computation shows that the differentials of these homotopies cancel exactly the unwanted composites of $B^1$. No $B^k$ for $k \ge 3$ is needed.
We now define a $A_\infty$ natural transformation of degree $0$
$$ \eta: \mathrm{Id} \to B. $$
We set
$$ \eta^0(T_1) = \eta^0(T_2) = \eta^0(T_3) = 0. $$
So objectwise, $\eta$ vanishes completely.
The only nonzero higher component is
$$ \eta^1(t_2) \in \mathrm{Hom}^{-1}(T_2, B(T_2)), $$
defined by the map
$$ T_2 \xrightarrow{t_2} T_2 $$
landing in the degree $-1$ term of $B(T_2)$. All other $\eta^1(f)$ vanish, and we set $\eta^k = 0$ for $k \ge 2$.
Finally, $\eta_{\mathrm{gen}}$ is not exact. Any degree $-1$ pre-natural transformation $h: Id \to B$ has only a possible objectwise component
$$ h^0_{T_2} = \alpha e_2 + \beta t_2, $$
and a direct computation shows that
$$ (dh)^1(t_2) = 0 $$
for all choices of $\alpha,\beta$. Hence $\eta_{\mathrm{gen}}$ represents a nontrivial cohomology class.
Moral: natural transformations can be real sneaky — even if nothing happens on objects, genuinely new information can live entirely in higher components.