The Clive paper I linked to above actually tests Listeria monocytogenes and basically found wood was better than the plastics. Again, we're talking cutting boards here, so the food source is not sitting on the surface the whole time. They would be looking at how long things last once the product is removed from the surface (and they seem to be showing that by 3 minutes after removal the wood surface showed reduced contamination compared to the plastic surfaces). This is well outside my area of expertise, so I can't evaluate the methodology, and I've not spent a lot of time on reading the article (skimmed to find the results section, etc), but at first blush it seems pretty clear that this evidence (i.e. this one paper) would suggest wood is superior at least to plastic. I would think the cheese industry, if they were concerned that this regulation is negatively influencing product quality and putting consumers at greater risk, could request independent reseach from Universities into best practice. The funding, if any, would have to be given in a way that keeps the University free from influence of either the FDA or the cheesemaking industry (i.e. we'll financially support a PhD or two on this topic, but other than indicating the area of interest, the research and IP that results remains with the University and the PhD, so publish no matter what you find).
Also, the differences we're talking about with cutting boards, at least, are not just differences in the lab but the effects are big enough to suggest differences in actual health risks (which the FDA is concerned with). Note the first link I included above ends by mentioning a consumer risk study where they found people with wooden cutting boards were at 1/2 the risk of salmonella poisoning compared to those using plastic ones. Meaning, the plastic boards are potentially a greater health risk than the wooden ones. It's possible the same could be true for cheese aging shelves, or there might be no difference, or the wooden ones might be worse, without proper study, it's all just guess work. Guess work is a pretty expensive way to make decisions.
If the study found the wooden shelves provided protection, the Cheese Industry could then push for clarification on why the FDA is pressuring them to put consumer's at risk. This is harder to argue if there is no difference (a possible outcome), and obviously, if the study were to show that wooden shelves were a risk, then the FDA is right to prevent an industry from putting people at unnecessary and measurable risk.