How do I fix this so that the connecting part doesn't overlap or leave gaps in between?
The object consists only of edges, and the problem occurs when more than 2 vertices are connected.
This is how it looks when Geometry Nodes are applied.
The right bar is what I'm aiming for. As you can see, the edges are aligned with the cube in the corner:
Unfortunately, I don't know your mesh, so I can only make guesses, but you could solve this as follows:
First split the mesh into single edges.
Then calculate the length of the edges and scale them inwards according to the desired thickness.
Turn these edges into curves with Mesh to Curve, and then back into a mesh with Curve to Mesh and a profile.
Next, instantiate cubes at the vertices of the original mesh. This will give you the basic shape.
So that the cubes do not have unnecessary faces, remove them by creating a selection. If the faces are exactly on the endpoints of the scaled edges, then it is an inner face and you can delete it.
Finally, you just need to combine this geometry, and merge the duplicate points with Merge by Distance.
PS: Of course, this technique only works for rectangular structures!
