Non-black-hole matter – more precisely one in which the curvature may be considered a small perturbation everywhere – always has a volume-extensive entropy that scales like $R^3$. It follows from the locality. In various condensed-matter systems, one may develop environments with various long-distance correlations that make the entropy non-extensive and may replace $R^3$ by $R^n$ with rather general fractional powers.
The scaling of the entropy as $R^2$ applies to the maximum entropy that can be squeezed into a given region, and the maximum entropy of a localized/squeezed system is the black hole entropy. The most fundamental laws of physics are those that can describe the most general state or conditions i.e. the highest entropy. And those fundamental laws see the $R^2$ upper bound on the entropy which is the entropy counting supporting the holographic nature of the Universe. Whether some lower-entropy (non-gravitational) systems with a volume-extensive entropy exist is irrelevant and doesn't create any contradiction; instead, this fact known for centuries is what makes the holographic principle non-trivial and powerful.
Holography only starts to affect physical objects "intensely" in the quantum gravity regime – but it does so and it is an important fact because the quantum gravity regime is one in which the fundamental laws are seen most clearly and without any approximations.