Berardi's original point was that, when overeating to gain muscle, limit fat gain by avoiding meals HIGH in both carbs and fat at the same time.
People took this concept way overboard, obsessing about every gram of fat in a P+C meal or every gram of carb in a P+F meal.
I have done a lot of self-experimentation (monitoring BF with calipers, diet with Fitday, and tracking it all in Excel). I think Berardi was right about this concept. Also looking at other bodybuilders on this site and elsewhere, separating fats and carbs is a common theme.
The concept makes a lot of sense. Glucose is the preferred fuel. If it's available, it will be used, and fats are more likely to be stored. Fats are stored as body fat much more easily than carbs. So you don't want to give your body a huge load of carbs/glucose, at the same time as a big load of fat, especially when you are overeating to gain muscle.
For dieting for fat loss, I don't think separating carbs and fats is that important, because you're NEVER eating meals HIGH in both. By definition when dieting, your meals are small. Insulin is very sensitive to portion size, so insulin will be lower even if the carb ratio of a small diet meal is high. But in any case, calorie deficit trumps everything else. I've done low-fat, low-carb, Zone-ish, carb cycling...they all work.
OP, I think you have some incorrect ideas...carbs are carbs. If you eat 100 g of a low-GI carb, it will still get broken down to glucose (and maybe some indigestible fiber). A large load of low-GI carbs can raise insulin for hours. An example of this would be oatmeal. Diabetics using exogenous insulin complain that though oatmeal is recommended to them as a healthy, whole-grain, complex carb, it still requires a lot of insulin.
Second, I don't know why you are concerned about water retention. Carbs do retain water, lots of it, low-GI or not. However, why is this a problem? You can experiment and see if different carb sources affect water retention differently. I have never noticed a difference except with Biotest's magic carbs that pull water into muscle.