Let $q:=4$. You are factorizing $X^{q^2}-X$ over $\mathbb{F}_q$. Thus, you should expect that $$X^{q^2}-X=(X^q-X)\,f_1(X)\,f_2(X)\,\cdots\,f_k(X)$$
where $f_1(X),f_2(X),\ldots,f_k(X)\in\mathbb{F}_q[X]$ are all the irreducible monic quadratic polynomials over $\mathbb{F}_q$ (whence $k=\dfrac{q^2-q}{2}$, which equals $6$ when $q=4$). You are right that the quadratic polynomial $X^2+X+1$ factors into linear terms over $\mathbb{F}_q=\mathbb{F}_4$, namely,
$$X^q-X=X^4-X=X(X+1)(X^2+X+1)=X(X+1)(X+t)(X+t+1)\,,$$
where $t$ is an element of $\mathbb{F}_4\setminus\mathbb{F}_2$.
Therefore, you have to find $6$ polynomials of the form
$$X^2+aX+b\,,$$
with $a,b\in\mathbb{F}_4=\{0,1,t,t+1\}$, that are not divisible by $X$, $X+1$, $X+t$, or $X+t+1$. If $a=0$, then note that every element of $\mathbb{F}_4$ is a square ($0=0^2$, $1=1^2$, $t=(t+1)^2$, and $t+1=t^2$), so $b=c^2$ for some $c\in\mathbb{F}_4$, and $X^2+aX+b=(X+c)^2$. Therefore, $a\neq 0$.
If $a=1$, then $b\in\{t,t+1\}$, and both choices work. If $a=t$, then $b\in\{1,t\}$ and both choices work. If $a=t+1$, then $b\in\{1,t+1\}$ and both choices work. This shows that
$$\begin{align}X^{16}-X&=X(X+1)(X+t)\big(X+(t+1)\big)\,(X^2+X+t)\,\big(X^2+X+(t+1)\big)\\&\phantom{abcf}(X^2+tX+1)\,(X^2+tX+t)\,\big(X^2+(t+1)\,X+1\big)\,\big(X^2+(t+1)\,X+(t+1)\big)\,.\end{align}$$
I cannot offer a good way to directly deal with the octic $X^8+X^7+X^5+X^4+X^3+X+1$, except from the work above. However, there is an easy way to factor the quartic polynomial $X^4+X^3+X^2+X+1$. Let $Y:=X+\dfrac{1}{X}$. Then,
$$\begin{align}X^4+X^3+X^2+X+1&=X^2\,(Y^2+Y+1)=X^2(Y+t)(Y+t+1)\\&=(X^2+tX+1)\,\big(X^2+(t+1)X+1\big)\,.\end{align}$$