You are asking about the **embedding of a graph structure into 3-space** $\mathbb{R}^3$. A graph structure by itself does not specify its embedding into $n$-space. In chemistry, these two different chiral instances of (tetrahedral) molecules below would be called stereo-isomers or enantiomers of each other.

In mechanical engineering, you'd be talking about building trusses and support structures, and a lot is known about the fact that quadrilaterals do not define a rigid structure. Quadrilaterals are easily sheared within a plane, and are not restricted to being coplanar, whereas triangular faces are at least limited to being coplanar.

Also, the presence of these constraints (on edge length and vertex-edge connectivity) also does not mean that it would be impossible to build partial structures that meet the specified partial constraints but which cannot be built upon to complete the structure. In other words, a "naive constructor" cold generate a partial assembly which is a configuration which is impossible to continue onto a final desired construction. There could be **dead-end** partial constructions which could not be completed. This type of problem could partially be avoided by also imposing a temporal constraint, or a sequence constraint, e.g. first add this, then add that.

However, there are chirality issues in play which cannot be avoided.

If the "vertices" do not impose restrictions on relative angles, then there are no additional contraints beyond edge-length, and the graph-structure and edge lengths will not usually define a single embedding in 3-space, relative to transformations such as translation and rotation.

If by topology, you do not also mean chirality, you may be correct. If you allow chirality differences to mean something, then there is a simple counterexample in the tetrahedron.

Let this tetrahedron $T_1$ in $\mathbb{R}^3$ be defined with a base triangle $ABC$ with the points $A=(0,0,0), B=(0,1,0), C=(1,0,0)$ and the top of the tetrahedron at $D=(0,0,1)$. Let the edge lengths of the skeleton of this polytope be defined based on this baseline instantiation in 3-space, $|AB|=1, |AC|=1, |BC|=\sqrt{2}, |AD|=1, |BD|=\sqrt{2}, |CD|=\sqrt{2}$.

Now note that if $D$ is instead placed at $D_2=(0,0,-1)$, that the this alternate tetrahedron (let's call it $T_2=ABCD_2$), has the same edge lengths as $T_1$, but has the mirror chirality. If we labeled the vertices with $A,B,C,D$, it is not possible to rotate and translate $T_1$ into $T_2$, whereas it is possible to turn $T_1$ inside-out and transform it into $T_2$.

If you don't have all triangular faces, e.g. you use the edge lengths of a cube as the only constraints on a skeleton of a cube, you'll quickly see the problem that engineers found in constructing trusses with square faces: parallelograms are not necessarily "rigid" and can be sheared easily and still maintain the correct edge-lengths between vertices. Thus it's not possible to build a rigid skelton with only square faces.

Thus, it depends on the axiomatic construction of your objects:

if you disallow disassembly and reconstruction, then the tetrahedra $T_1$ and $T_2$ are separate chiral mirror-images of each other. If you allow for disassembly and reconstruction, then $T_1$ and $T_2$ have the same topology. If you also define "topologically equivalent" to allow for elastic stretching (at least for transforming from one 3-d realization to another, then back to being solid and rigid while in a specific 3-d realization), then $T_1$ can be transformed into $T_2$ by pushing the vertex $D$ through the center of the face $ABC$ and onto the other side. If the faces actually have a physical planar object defining that face (like a kite has its tissue paper), then this sort of transform is disallowed and the mirror image tetrahedra $T_1$ and $T_2$ are different.

You can also visualize this by allowing the edges to be made of elastic springy rods with spring constants $k_i$. If the $k$'s are very large, then the springs are very stiff and the inversion will be impossible; if the $k$'s are small, the springs have a lot of give and it's easily possible to change between the two mirror-image configurations.

potentiallybe possible to fix the edge lengths and connectivity constraints for a skeleton graph for some convex polytope, then reconfigure the graph (we don't care how this happens) into a knotted configuration without violating those constraints. $\endgroup$