rmx This is just an example from my own experience, but I often take the approach of setting the vertices radially, similar to the first example you mentioned.
The reason is that, as shown in your screenshot, there are often shadowed areas where a radial layout tends to create smoother connections.
On the other hand, in one of the official example skeletons, mix-and-match
, the vertices are connected in a straight line, similar to the second example you mentioned:

In this skeleton, the arms and legs are designed to bend in a rounded manner, so connecting the vertices this way makes sense:

As Spinebot mentioned, the appropriate way to set up vertices and edges depends on the kind of movement you want to achieve, so it’s difficult to give a one-size-fits-all answer.
I hope this helps in some way!