I don't know how we can escape the conclusion that that unique frame of reference tells us what the universe is actually doing.
Very, very easily.
First, it's not unique even if we ignore the fact that there are perturbations (see my reply to Zig above).
Second, there
are perturbations which destroy the whole concept of a precise unique frame. The universe is
not homogeneous and isotropic, it's just
approximately so, and even that only on a particular range of scales.
Third, we can only see part of the universe, and have no evidence at all that the perturbations remain small on larger scales (i.e. no reason to think it remains approximately homogeneous and isotropic on larger than horizon scales).
Fourth, even if we ignore all of the above, your objection would only make sense if there was only one possibility - if the universe must
always have that unique frame. But we know for certain that isn't true (because there are perturbations, and because everything we know about physics says it isn't).
Fifth, even if we ignore all of the above, the ability of GR to describe more than one frame is a feature without which it would simply be incomplete. Asking that it only be able to describe physics in one special frame is like asking for a theory of linguistics that only works on one language, or requiring that map-making theory only admit one projection, or that arithmetic only work in Roman numerals... it's utter nonsense.
The whole
point of GR - the stroke of genius that led to it - was Einstein's realization that physics cannot possibly depend on the coordinates we humans choose to describe it with, and that following that fact through actually carries profound and mathematically powerful consequences.