1. People rarely compare it directly to something like a "Real Food" diet - they go from a lot of processed crap to mostly non processed stuff on the outside of the grocery store and then see huge benefits. But I suspect if they just switched to a Real Food diet in the first place they would see most of the same benefits.
2. It completely leaves out almost all legumes and many root vegetables and gourds which are both hugely beneficial and also some of the cheapest / most sustainable calories out there. There is a reason humans domesticated gourds early on - they are easy as hell to grow, tasty, healthy, balanced, and the shells often also provide other benefits.
On top of that the three above food groups are the main sources of high quality prebiotics (not probiotics) which are essential to our gut health and producing both essential fatty acids and Vitamin K2. The FDA just assumes that people meet an RDA value for EFA and K2 based on gut fermentation but this relies on people consuming quality fiber and most importantly specific prebiotics like long chain inulin and resistant starch (which are very different than simple starch and normal inulin). EFA and K2 are intricately involved in immune modulation, gut inflammation, inflammation in general, and all kinds of other processes.
I think we all know that the average person in the west is likely not eating nearly enough of these prebiotics and in addition many have other digestion issues as well. There is a reason scientists call them ESSENTIAL fatty acids and not "kinda sorta important" fatty acids.