According to the AI overview, so take it for what it’s worth, on a low carb diet, muscle glycogen gets replaced via gluconeogenesis from non carbohydrate sources such as amino acids and glycerol.
I remember reading some time ago, that for one who exercises once a day, the rate of glycogen replacement on low carb is just fine. For those higher level athletes who exercise twice a day, eating carbs after the workout helps replenish the muscles more quickly for the next round of exercise.
The overview also mentioned that as the body gets fat adapted, it becomes more efficient at gluconeogenesis and so it can replenish the muscles more quickly. That seems to fit with the paper you referenced.
*"Compared to highly trained ultra-endurance athletes consuming an HC diet, long-term keto-adaptation results in extraordinarily high rates of fat oxidation, whereas muscle glycogen utilization and repletion patterns during and after a 3 hour run are similar."*