Yes it is related to performance.
We do use skeleton parts as well. But we use them more to have the different sub-assemblies defined according to origo.
Basically we have a sketches on different planes on the skeleton planes. To keep the overview. And then each sub-assembly has the skeleton part as its first part.
In this way we use the skeleton part to keep the design overview, basically we just use it for placement (make an external mate to place it and then delete the external mate, and remating it to the 3 standard planes). This also allow us to compare any sub-assemblies in a new assembly, by simply dragging them into origo.
We have to do this to have a chance to work at all. When done with the construction, we make as-build parts of the assemblies and collect these in a top assembly (saving each assembly as a part). Otherwise we cannot open it. We just made one of the biggest Flexo Printers in the world, and are just working on being able to make some top-assemblies that can be used for documentation.
Our sub-assemblies can be up to 10k parts, and the top assembly could be more than 100k parts (though only 15k different parts).
For those interested, please take a peak :-)