It's almost like your body has a bunch of internal processes to maintain homeostasis around crucial functions, and maintaining the appropriate osmotic pressure is essential to life. Yes, this feedback loop has a little lag, so you can die from water intoxication, and/or hold water weight from a particularly salty meal (or one with a lot of carbohydrates if you don't often consume them, since cell volume is largely water, and increased glycogen storage will knock it out of balance for a bit). Assuming your diet is reasonably homogenous, your body is not packing on 400% of the weight of carbohydrates in added water. It's using the carbohydrates to replenish glycogen stores in your liver and muscles via insulin. If those stores are not depleted, it'll get converted into fatty acids via de novo lipogenesis. When you're asleep or between meals, glucagon will take glycogen back out of your liver for use, and if that depletes, some catecholamine will trigger lipolysis to do it from stored triglycerides made from the fatty acids.

It does not assume that every molecule is metabolized homogenously, nor that your body is perfectly efficient, and not even that everyone's body has the same level of efficiency.

It more or less means "track how many calories you are eating to get a baseline number. If you want to lose weight, decrease that number. If you want to gain weight, increase that number. Continue tracking until you establish a baseline number for whatever weight you wantwhen you have reached it".

Your digestive system generally does NOT "happily pass unwanted calories without absorption". Ingested fat is broken down into long chain fatty acids, which can be stored directly in adipose tissue with no further metabolic changes. If you consume a ton of fats at one time, there flat-out may not be enough bile salts released to emulsify it all down, and/or not enough pancreatic lipase released to turn all of the emulsified fats into fatty acids, and/or not enough time for them all to be absorbed in your small intestine. Statements like that are more or less like saying "Battletoads players will happily smash into barriers on bikes/surfboards/planes/clinger-winger", or "internal combustion engines will happily pass unburned fuel". It's a system in motion with a limited point of insertion (the common bile duct at the beginning of the duodenum), and hopefully long enough to finish the job. The fact that this is not always true just means that the system has been overloaded.

Gluconeogenesis from proteins is such a metabolically expensive process that your body does actually try to avoid that one, but it will if it has to, which is why rabbit starvation is true.

This post is peak overconfidence based on an amazingly shallow depth of knowledge.