This is not a solution. This is a reply to William's above comment, which said
"Have you already tried going through the proof of the original theorem, to see what might change if you replace 1 by 2 in the initial conditions?"
In order to make it easier to show the proof of the $6$-Somos sequence, I'm going to show that the $4$-Somos sequence always gives an integer.
The $4$-Somos sequence $\{c_n\}$ is defined as
$$\begin{align}c_{n+4}=\frac{c_{n+3}\cdot c_{n+1}+{c_{n+2}}^2}{c_{n}}\ \ (n\ge0)\qquad(1)\end{align}$$
$$c_0=c_1=c_2=c_3=1.$$
Note that it is sufficient to prove the following theorem :
Theorem : Let $c_0=w,c_1=x,c_2=y,c_3=z$ be variables, and let $\frac{p_n}{q_n}$ be the rational expression of $c_n$ with irreducible representation by $(1)$. Then, the denominator of $q_n$ is always a monomial expression about $w,x,y,z$ whose coefficient is $1$.
Proof : The $n\le 7$ cases are obvious. The point is the $n=8$ case. Let $A$ be $p_4=xz+y^2$. Noting that $q_5=wx,q_6=w^2xy,q_7=w^3x^2yz$, we get
$$p_5=Ay+z^2w, p_6=A^2x+Ayzw+z^3w^2,$$$$ p_7=A^3(x^2+yw)+A^2z^2w^2+Ay^2z^2w^2+yz^4w^3.$$
Hence, we know that $p_4$ is coprime to each of $p_5,p_6,p_7$ (as a polynomial). Since the constant term of the numerator of $c_8$ is $y^2z^6w^4+xz^7w^4=z^6w^4A,$ we know that the numerator of $c_8$, as a whole, can be divided by $A=p_4$. By induction, treating $c_9$ as $c_8$ which starts from $x,y,z,a=\frac{A}{w}$, by the same argument above, we know that the denominator is a monomial expression only with $w,x,y,z$ and so on. Now the proof is completed.
Now, I'm going to show the proof of the $6$-Somos sequence briefly. It is known that this proof is completed by using Macsyma. (by Dean Hickerson)
The way of this proof is the same as above.
See $a_n$ as the rational function about
$$a_0=u, a_1=v, a_2=w, a_3=x, a_4=y, a_5=z,$$
and show that the denominator is always a monomial expression about $u,v,w,x,y,z$ whose coefficient is $1$ with irreducible representation. The point is to show every numerator can be represented as a polynomial of $B=vz+wy+x^2$. The difficulty lies in showing the constant term of the numerator of $a_{12}$, which is a polynomial with $194$ terms, can be represented by $B$.
(In my opinion, this way is something like "caluculations tells us this is true". As far as I know, the mystery that "why these can be divided?" still remains unsolved.)
Anyway, what I would like to say is that the above theorem (the way of thinking), which is all I know, is not sufficient to solve my question.