The following holonomic proof follows Peter Paule and Carsten Schneider's 2024 report Creative Telescoping for Hypergeometric Double Sums, and was generated using their software.
Denote the inner sum
$$f(r,a)=\sum_{b=0}^a\binom ab^2\binom{r+b}a=\sum_{b=0}^as(r,a,b)$$
and compute two recurrences for it:
In[1]:= << RISC`fastZeil`
<< Downloads/Sigma.m
In[5]:= sd = Binomial[a, b]^2 Binomial[r + b, a];
prerod = Zb[sd, {b, 0, a}, a];
rod = ReleaseHold[prerod[[1]]] /. SUM -> f
Out[5]= -(1 + a)^2 f[a] - (3 + 2 a) (1 + 2 r) f[1 + a] + (2 + a)^2 f[2 + a] == 0
In[7]:= {r0, r1, r2} = FunctionExpand[{sd, (sd /. r -> r + 1), (sd /. a -> a + 1)}/sd];
prehook = Gosper[sd, {b, 0, a}, Parameterized -> {r0, r1, r2}];
hook = ReleaseHold[prehook[[1, 1, 1]]] ==
0 /. {DisplayForm[SubscriptBox["F", "0"]][b] -> f[a],
DisplayForm[SubscriptBox["F", "1"]][b] -> f[r + 1, a],
DisplayForm[SubscriptBox["F", "2"]][b] -> f[a + 1]}
Out[7]= (-1 - a^2 - 2 r + 2 a r - 2 r^2) f[a] - (1 + a)^2 f[1 + a] +
2 (1 + r)^2 f[1 + r, a] == 0
$$(a+1)^2f(r,a)+(2a+3)(2r+1)f(r,a+1)-(a+2)^2f(r,a+2)=0$$
$$2(r+1)^2f(r+1,a)-(a^2-2ar+2r^2+2r+1)f(r,a)-(a+1)^2f(r,a+1)=0$$
The first recurrence has certificate (obtained using Prove[])
$$g(r,a,b)=\frac{(a+1)b^2(b-a+r)(2a^2-3ab-3ar+5a+b^2+2br-4b-6r+2)}{(b-a-2)^2(b-a-1)^2}s(r,a,b)$$
in the sense that the following telescoping equation holds:
$$(a+1)^2s(r,a,b)+(2a+3)(2r+1)s(r,a+1,b)-(a+2)^2s(r,a+2,b)=g(r,a,b+1)-g(r,a,b)$$
Dividing both sides by $s(r,a,b)$ results in an easily verifiable rational function identity. In exactly the same manner the second recurrence is certified by
$$g(r,a,b)=-\frac{b^2(a^2-ab-3ar-a+2br+b-3r-2)}{(a-b+1)^2}s(r,a,b)$$
Using these two recurrences we now compute one for $A(r)$:
In[9]:= CreativeTelescoping[
SigmaSum[Binomial[r, a]^2 f[a], {a, 0, r}], r, {{rod, f[a]}}, hook]
Out[9]= {{(1 + r)^3, -(1/4) (3 + 2 r) (7 + 9 r + 3 r^2),
1/16 (2 +
r)^3, ((80 + 8 a - 206 a^2 + 206 a^3 - 104 a^4 - 10 a^5 +
10 a^6 + 456 r + 160 a r - 1095 a^2 r + 843 a^3 r -
214 a^4 r - 25 a^5 r + 7 a^6 r + 1020 r^2 + 658 a r^2 -
2182 a^2 r^2 + 1172 a^3 r^2 - 160 a^4 r^2 - 12 a^5 r^2 +
1158 r^3 + 1114 a r^3 - 2054 a^2 r^3 + 696 a^3 r^3 -
44 a^4 r^3 + 708 r^4 + 916 a r^4 - 924 a^2 r^4 +
152 a^3 r^4 + 222 r^5 + 364 a r^5 - 160 a^2 r^5 + 28 r^6 +
56 a r^6) f[a] Binomial[r, a]^2)/(32 (-2 + a - r)^2 (-1 + a - r)^2) + ((1 +
a)^2 (-80 + 152 a - 98 a^2 - 10 a^3 + 10 a^4 - 296 r +
448 a r - 213 a^2 r - 5 a^3 r + 7 a^4 r - 428 r^2 +
486 a r^2 - 156 a^2 r^2 + 2 a^3 r^2 - 302 r^3 + 230 a r^3 -
38 a^2 r^3 - 104 r^4 + 40 a r^4 - 14 r^5) f[1 + a] Binomial[r, a]^2)/(32 (-2 + a - r)^2 (-1 + a - r)^2)}}
Call the gnarly fourth element of the output $h(r,a)$:
$$
\frac{\binom ra^2}{32(r-a+2)^2(r-a+1)^2}
\left(\begin{bmatrix}
80 & 8 & -206 & 206 & -104 & -10 & 10 \\
456 & 160 & -1095 & 843 & -214 & -25 & 7 \\
1020 & 658 & -2182 & 1172 & -160 & -12 \\
1158 & 1114 & -2054 & 696 & -44 \\
708 & 916 & -924 & 152 \\
222 & 364 & -160 \\
28 & 56
\end{bmatrix}f(r,a) +
(1+a)^2\begin{bmatrix}
-80 & 152 & -98 & -10 & 10 \\
-296 & 448 & -213 & -5 & 7 \\
-428 & 486 & -156 & 2 \\
-302 & 230 & -38 \\
-104 & 40 \\
-14
\end{bmatrix}f(r,a+1)\right)$$
The matrices are shorthand for polynomials whose $r^ia^j$ coefficient is $a_{ij}$, using 0-indexing. With the help of the two smaller recurrences we can verify
$$(r+1)^3\binom ra^2f(r,a)-\frac14(2r+3)(3r^2+9r+7)\binom{r+1}a^2f(r+1,a)+\frac1{16}(r+2)^3\binom{r+2}a^2f(r+2,a)=h(r,a+1)-h(r,a)$$
which telescopes to
$$(r+1)^3A(r)-\frac14(2r+3)(3r^2+9r+7)A(r+1)+\frac1{16}(r+2)^3A(r+2)=0$$
But $B(r)$ satisfies the same recurrence, and the first two terms of $A(r)$ and $B(r)$ agree. This proves $A=B$.