If you re-rig the figure in the setup room then you likely won't be able to use many of the morphs++ features from the original M4. 

Also if you re-rig the figure then you will have to transfer the new rig to every piece of clothing you want to use, and some clothing has extra control bones so those would have to be rebuilt as well. 

So I would say using animatable joint centers would be your best bet. Those can be transferred to clothing without affecting the rest of the clothing rig (if it has extra bones). 

There is no advantage to using the default pose for M4, it's just the way that morphs work. The default pose is the pose that M4 was modeled in and loads into Poser in. So morphs and clothing built for him have to be built using that pose. You can change the pose and morph the figure from the changed pose, but there's a lot more work involved with reversing the morph back to M4's default pose.