This is not the question you want to ask. (The actual question asked is easy by a continuity argument.) If the sides of the pyramid have length $2r$ and the height is $h$, then the other side lengths of the pyramid have length $\sqrt{2r^2 + h^2}$. You want to ask whether the element

$$\xi = (2r \otimes \theta) + (\sqrt{h^2 + 2 r^2} \otimes \phi)$$

is trivial in the Dehn group. For this to be true, either:

1. $\theta$ and $\phi$ are both rational multiples of $\pi$ (case already done).
2. $r$ is a rational multiple $0 < v < 1/\sqrt{2}$ of $\sqrt{h^2 + 2 r^2}$, and so

$$\xi = \sqrt{h^2 + 2 r^2} \otimes (2 v \theta + \phi);$$

then one moreover demands $2 v \theta + \phi$ is a rational multiple of $\pi$. This is a much more stringent requirement. In fact, it never happens, by the following elementary but tedious argument.

By scaling, we can assume that $h = 1$. Hence it follows that $r^2$ is a rational multiple of $1 + 2 r^2$, which certainly implies that $r^2$ is rational. So let $r^2 = t$. Thus we require that

$$\frac{r}{\sqrt{1 + 2 r^2}} = \sqrt{\frac{t}{1 + 2 t}} = v$$

is rational. It follows that we have $$r^2 = t = \frac{v^2}{1 - 2 v^2}$$ for some rational $v$. Thus we can rephrase the problem as follows:

Find all rational $0 < v < 1/\sqrt{2}$ with $$\cos(\theta) = \frac{r}{\sqrt{r^2 + 1}} = \frac{v}{\sqrt{1 - v^2}},$$ $$\cos(\phi) = \frac{-r^2}{r^2 + 1} = \frac{-v^2}{1 - v^2},$$ and such that $$(2 v \theta + \phi) \in {\mathbf{Q}} \pi.$$

Let us do an example to explain how one can eliminate any specific $v$. Take the case of $v = 1/2$. We find that $$\cos(\theta) = 1/\sqrt{3}, \quad \cos(\phi) = -1/3,$$ from which we deduce (for example) that $$\cos(2 v \theta + \phi) = \cos(\theta + \phi) = - \frac{5}{3 \sqrt{3}}.$$ If $\alpha = 2v \theta + \phi$ is a multiple of $\pi$, then $$\cos(\alpha) = \frac{\zeta + \zeta^{-1}}{2},$$ where $\zeta = e^{i \alpha}$ is a root of unity. But knowing $\cos(\alpha)$ one can solve for $\zeta$ and then determine if it is a root of unity or not from its minimal polynomial. In the example above, we win immediately because $2 \cos(\alpha)$ should be an algebraic integer and it is not. The cases $v = 1/3$ and $v = 2/5$ can be handled in a very similar way: if $v = 1/3$, then $\cos(\theta) = 1/(2 \sqrt{2})$ and $\cos(\phi) = -1/8$, and, with $\alpha = 3 (2v \theta + \phi)$, $$\cos(\alpha) = \cos(2 \theta + 3 \phi) = \frac{87}{256},$$ and if $v = 3/5$, then $\cos(\theta) = 3/5$ and $\cos(\phi) =9/25$, and with $\alpha = 5 (2v \theta + \phi)$, $$\cos(\alpha) = \cos(6 \theta + 5 \phi) = \frac{3617721}{4194304}.$$ In both cases, the corresponding $\zeta$ is manifestly not a root of unity because $2 \cos(\alpha)$ is not an algebraic integer.

Returning to the original problem, the first thing we will do is prove that ${\mathbf{Q}}(e^{2 v i \theta})$ is an abelian extension. We may write $$e^{2 v i \theta} = e^{(2 v \theta + \phi) i} \cdot e^{- \phi i}.$$ Since $2 v \theta + \phi \in {\mathbf{Q}} \pi$, the first factor is a root of unity and so lies in an abelian extension. On the other hand, the second term is simply $$\cos(\phi) - i \cdot \sin(\phi).$$ Since $\cos(\phi) \in {\mathbf{Q}}$, it follows that $i \cdot \sin(\phi) = \sqrt{\cos^2(\phi) - 1}$ lives in an imaginary quadratic extension of ${\mathbf{Q}}$. In particular, $e^{- i \phi}$ clearly lies inside an abelian extension. Taken together, we deduce:

The extension ${\mathbf{Q}}(e^{2 v i \theta})$ is abelian.

We also have the explicit formulae $$e^{i \theta} = \cos(\theta) + i \sin(\theta) = \frac{v + i \sqrt{1 - 2 v^2}}{\sqrt{1 - v^2}},$$ and then squaring: $$e^{2 i \theta} = \frac{ 3 v^2 - 1 + 2 v \sqrt{2 v^2 - 1}}{1 - v^2}.$$

Let $v = a/b$ with $(a,b) = 1$, this becomes $$e^{2 i \theta} = \frac{ 3 a^2 - b^2 + 2 a \sqrt{2 a^2 - b^2 }}{(b^2 - a^2)}.$$ Let $E = {\mathbf{Q}}(\sqrt{2 a^2 - b^2 })$, which is an imaginary quadratic extension of ${\mathbf{Q}}$. (The condition that $a/b = v < 1/\sqrt{2}$ implies that $b^2 > 2 a^2$.) Let us write $$x = 3 a^2 - b^2 + 2 a \sqrt{2 a^2 - b^2 } \in \mathcal{O}_E.$$ Note that $N(x) = (b^2 - a^2)^2$. Secondly, note that $$e^{2 v i \theta} = (e^{2 i a\theta})^{1/b}$$

By Galois theory, $E(\alpha^{1/b})$ can only be an abelian extension of ${\mathbf{Q}}$ (or even of $E$) under the following conditions:

1. $\alpha$ is a perfect $b$th power in $E$.
2. $b$ is even and $\alpha$ is a perfect $b/2$th power in $E$.

Moreover, since$(a,b) = 1$, if $e^{2 i a \theta}$ is a perfect $b$ or $b/2$th power, then so is $e^{2 i \theta}$. In particular, $e^{4 i \theta}$ is a $b$th power in $E$. Note also that $$e^{4 i \theta} = \frac{x^2}{N(x)} = \frac{x^2}{x \overline{x}} = \frac{x}{\overline{x}},$$ so $x/\overline{x}$ is a perfect $b$th power in $E$. Our goal is now to prove that the ideal $(x)$ is (almost) a $b$th power, and deduce that $N(x) = (b^2 - a^2)^2$ is (almost) a $b$th power.

Suppose that $\mathfrak{p}$ is a prime ideal of $\mathcal{O}_E$ which divides both $x$ and $\overline{x}$. I claim that $\mathfrak{p}$ divides $2$. Note that $N(x) = (b^2 - a^2)^2$, so so $a^2 \equiv b^2 \mod \mathfrak{p}$. But then $$x + \overline{x} = 2(3 a^2 - b^2) \equiv 4 a^2 \mod \mathfrak{p}.$$ If $a \in \mathfrak{p}$ then also $b \in \mathfrak{p}$ contradicting that $(a,b) = 1$. Hence $(x,\overline{x})$ is only divisible by primes above $2$. Since $x/\overline{x}$ is a $b$th power, and $(x,\overline{x})$ is supported at primes above $2$, we deduce that $(x) = I^b \cdot J$ where $J$ is supported at primes above $2$. We deduce that

$$N(x) = (b^2 - a^2)^2 = n^b \cdot 2^k.$$

where $n$ is an odd integer. Let us first consider the case when $a$ and $b$ are not both odd. In this case $k$ is trivial, and $(b^2 - a^2)^2 = n^b$. Since $b^2 - a^2 = 1$ has no solutions in positive integers, it follows that $b^2 - a^2 > 1$, but then $$b^4 > (b^2 - a^2)^2 \ge 2^b,$$ from which we deduce that $b < 16$. Now suppose that $a$ and $b$ are both odd. Since $(b-a,a+b) = 2$ in this case, it must be the case that $$b-a = r^b 2^u, b+a = s^b 2^v,$$ where one of $u$ and $v$ must be equal to $1$.

1. Case 1: $u = 1$. If $b-a=2$, then from the inequality $v < 1/\sqrt{2}$ and $a < b/\sqrt{2}$, we deduce that $$2 = b - a > b(1 - 1/\sqrt{2}),$$ and thus $b < 7$. If $b-a=2 \cdot r^b$ with $r > 1$, then $$b \ge b - a \ge 2^{b+1},$$ which is impossible.

2. Case 2: $v = 1$. We have $a+b = 2 \cdot s^b$, and now $$2b > a + b \ge 2^{b+1},$$ which once again is impossible.

Putting this together, we deduce that $b < 16$. Checking all the cases with $b < 16$ (noting that $a/b < 1/\sqrt{2}$ and $(a,b) = 1$) we find that the only possible pairs are $$(a,b) = (1,2), (1,3), (3,5), \ \text{or} \ v =1/2, 1/3, 3/5.$$ But these cases have already been considered previously.