Gluconeogenesis starts when liver stores hit 50-60% of maximal, and that happens about 2-3 hours after you last ate and the carbs have stopped absorbing. With proper food choices this is usually 6-7 hours or so after the meal, but for most people it's more like 4 because of the much faster absorption of refined carbs. Believe it or not, if you have a large insulin spike that leads to excessively rapid nutrient storage that can happen sooner.
The research that leangains is built upon specifically notes that liver glycogen utilization is significantly reduced by 3 hours after eating. Interesting. It also notes that there is a somewhat greater reliance on body fat for energy, but the body fat has to be burned in a carbohydrate flame, so to speak. Those carbs have to come from somewhere, and when it isn't the liver glycogen it's gluconeogenesis. It is technically true that the glycerol backbone of triglycerides can be burned, but you need to burn 100g of fat to get 10g of glycerol. That's 900 calories for 40 calories of sugar substitute. That's about 1.3g per hour, and that's not even close to enough to feed the brain.
So yes, assuming 100% of the excess goes to storage is seemingly a large assumption, but stop and think: I just ate 50% of my calories in one sitting. That's 1600 calories. I burn 133 an hour when awake. I'm pretty sure that even assuming a 6 hour absorption window with a perfectly flat absorption curve you can see how that would be 3x beyond what my body can use, yes? Now consider the enormous insulin response that this kind of eating generates. Insulin accelerates nutrient absorption, and in this case makes nutrient overload even worse. There is a large spike of available calories, and what happens is that these excess calories (those that can not be processed in the moment) get stored as fat. There is nowhere else to put them, glycogen can only be regenerated so quickly. There's only about 1500g of glycogen in the average man, so say 2000g in me. Research shows it takes 72 hours to replenish glycogen from a depleted state (which is when the process is most rapid), so if we do some math that means I can store a MAXIMUM of 27.7g of glycogen per hour. That is 111.1 excess carbohydrate calories. So even in that very exciting ideal scenario, assuming a 6 hour absortion window, that's 666.6 excess calories. Many of those are not carbohydrate. The protein can't be efficiently converted to glycogen, that has been measured at a maximum rate of about 200g per day or 10g of glycogen per 17.2g of protein per hour (using the known 1.72:1 protein to glucose ratio).
How do you want it? Even if there were 80g of excess protein, that's only 46.5g of glycogen. 200 calories. I'll burn that while I sleep and then some. My body's going to have so much excess carbohydrate that the known rate of ~40% of excess carbs turning to fat is a reliable starting point, and 100% of the dietary fat will either be absorbed and stored without being used for energy or will simply spare the exact same amount of body fat, leading to the same net accumulation either way due to there being zero loss if we assume that only dietary fat is being burned during that time. During the same time, regardless of source a maximum of 166.2g of muscle glycogen can be replenished in that time. That's barely what I used in the workout, and in a best case scenario. Where do the excess calories go? Into fat. We both know best case scenarios aren't how things work, so we can assume that if the best case scenario shows that under unrealistically good conditions 664 calories are stored as glycogen and 798 are burned as energy. That leaves 142 calories to be stored as fat, which wouldn't be that bad.
Unfortunately, that's not how insulin does its job. There is going to be a very large initial surge in the blood, which is going to lead to nearly everything being stored as fat in the first hour or two, representing 3-400 calories all by itself at minimum. Realistically, a bit more. By the 3rd hour absorption rate should have slowed enough to where blood sugar is a bit more stable and the insulin response dies down a bit, but you're still going to have more to deal with per hour than the body can handle.
Everything that is stored as fat can't be used as carbs OR converted to glycogen, which reduces those ideal numbers quite a bit. So it is absolutely fair, based on known hormonal responses, to state that nearly all of that excess is going to go into body fat.
The time under the curves clearly shows that there is still a net loss of body fat, on the order of 39% more than the surplus or so. Assuming the surplus is 600 kcalories, that's a 234 kcal loss. That works out to about 2 lbs of pure body fat gone every 30 days. Common results with leangains aren't ridiculously far beyond that, especially when you factor in the water weight that people initially shed. 10 lbs lost in 12-14 weeks is the norm, and assuming just a 2 lb loss of water weight due to getting what is usually excessive fast carbs and excess sodium out of the diet that's 8 lbs in 84-98 days. That's 313 calories of fat lost per day at 92 days on average. 33% more than calculated, but not bad for a ballpark figure. It is also assuming a fairly small amount of water weight lost, and completely strict adherence to Martin's personal coaching guidelines. Those are the results his personal clients tend to see, and to be perfectly honest those are great results when you consider that there is basically zero lean mass loss and non-morbidly obese clients. Could be better, but people consistently do well and on that I gladly give credit.
I am looking into the rumors of IF being accused of being a risk factor for diabetes. I wouldn't be terribly surprised, as research shows significantly higher insulin resistance when people eat 3x per day instead of 6-8x per day. In that sense, it would be a risk factor. As Martin advocates a body part split for workouts, it is also possible that this limits the benefits of exercise-induced insulin re-sensitization as the benefits typically only last for a few days so not all of the body is being re-sensitized all the time. You sort of do this merry-go-round thing.
You'll also notice that HDL counts seem to go down, according to the numbers I have seen posted by his clients on his site, which is not exactly ideal. This is related to his fairly well-known adversity towards cardio, as cardio is the only consistently proven way to increase HDL counts. Makes sense, if you think about the function of HDL: It pulls fats out of the blood. If you're doing long, steady-state aerobic training you need more of these particles to get the fat to your slow twitch fibers.
To be perfectly fair, their other numbers like LDL and triglycerides take a divebomb by comparison, so their HDL to triglyceride and LDL ratios improve immensely. That is simply something I want to point out.
Health requires more than just aesthetic perfection.