Think about how a client would like it, I would keep them as separate objects as it allows for easier animation. Or maybe, only join the parts that are actually meant to be fixed together in the real world one.
About the extensions, why not upload both formats? You can upload in as many different formats as you want, then the client chooses to download which one suits his needs.
Usually, in my blend files I simply include the models with the textures and material already set up.