Now there is a caveat to this. You only need to be exposed to things like gluten once every ten to fifteen days to keep the gut damaged. This can bedevil people as they “cut back on gluten” but do not notice an improvement in their overall health. I’m sorry but there is not a pink “participant” ribbon given out for doing this “almost correctly.” You need to be 100 percent compliant for thirty days, then see how you do with reintroduction.
As for: Is it the fact that you are likely eating more fiber and nutrients? Is it a difference in blood sugar levels that you notice?
Those are both directly related to what you are eating. I feel better when my blood sugar levels don't spike -- which is why I'm eating paleo.
Also, you didn't really put for an argument as to why the advice to cut out foods then add them back in is bad. If your body has healed itself and is functioning great without grains, then you eat a big pizza -- you will almost surely see how it affects your system.