Perhaps I'll restate the question for the OP, as it seems that people keep missing it.
When one derives the Friedmann equations using Newtonian framework, one picks an arbitrary point in a homogeneous and isotropic distribution of matter as the origin of their coordinates, and writes the equation for acceleration of a particle P at distance R from the origin, which is then converted to mechanical energy equation.
With some manipulation we arrive at the first Friedmann equation (steps detailed here:
http://www.astronomy.ohio-state.edu/~dhw/A5682/notes4.pdf).
The derivation uses Gauss' law (or equivalently: shell theorem), to justify that all matter located farther than R has no bearing on the dynamics of P.
Since the choice of a sphere drawn in the homogeneous distribution of matter was arbitrary, we should be able to describe the dynamics of the same particle w/r to a different point, and get exactly the same equation. So, if P was e.g. moving away and decelerating w/r to origin O, it does the same w/r to origin O'.
However, since this deceleration is governed by Newtonian gravity, what stops us from saying that point P has no force acting on it, since for any arbitrarily chosen origin we can choose another one, exactly opposite the first and at the same distance, w/r to which P is pulled with equal but opposite force.
Taking into account that in Newtonian derivation we are dealing with particles moving on a static spatial background (rather than embedded in expanding space as in GR), we have a particle that experiences 0 net force.
So what is the justification for saying that it does move w/r to any chosen point (i.e. the sphere of matter is self-gravitating)?
I.e., what gives us the right to write the first step in the derivation, where particle P is accelerated towards the arbitrary origin point?
I was thinking about an answer, but am not quite happy with my reasoning. The best I could come up with was that we get 0 acceleration only with a change of reference frame. As long as you stick with describing the dynamics within one frame, there's no problem. Which would mean that the 0 acceleration result is an error coming from trying to use two reference frames at once.
There's also the possibility that this is just one of the limitations of Newtonian derivation, and that one needs to follow the GR derivation to get rid of it in a satisfactory manner (after all, the Friedmann equations were only arrived at once GR was available). Not being conversant with GR I can't be certain that's the case, though. Furthermore, while browsing a couple papers detailing differences between the two derivations these past few days, this issue was never brought up.
If anyone can fill in the blanks, that'd be great.