there are a couple misconceptions in here.
your body does not wait to replenish glycogen until you eat a high carb meal. you don’t diminish glycogen without very intense exercise or starvation. once it is used up, the body replenishes it ASAP out of the substrates available. in a ketogenic eater that is the glucogenic amino acids (the ketogenic amino acids are dumped into the blood stream as fuel), glycerol and lactate . These are available as a product of the exercise you just did to deplete it. prior to exercise your body was maintaining blood sugar homeostasis via GNG from either glycerol or protein (if you were eating “excess” beyond repair/maintenance etc). glycogen replacement is prioritized after blood sugar homeostasis. replenishing the liver glycogen takes priority over muscle.
You do not excrete excess protein. the body does not “waste” it. it is partition into GNG in front of glycerol lactate etc once the bodies demands for it are met. it does this because if need arises then the amino acids can be directed away from GNG if needed.