I think there are individual differences, maybe dependent on your own degree of insulin sensitivity, on whether higher or lower carb diets work best for a person. But that aside, maybe you do need to up the calories to the level that she recommends on your exercise days. Then at least you will know whether you have an overtraining issue (too much exercise and not enough calories leading to burning of muscle). What seems odd to me is that you feel better and stronger but the data shows muscle loss. Weird.

There are so many variables as well as individual differences that I wonder how anyone can give good advice. All you can do is play at it, paying attention and giving enough time for each experiment to work.

I have substantially increased my calories, both carbs and protein, but not fat, and suddenly I am getting strength gains from the weight training that I do. My issue is getting the sweet spot in calories. My weight is trending up just a hair so I have cut it back a bit. I think I have been running a 100 to 200 excess. But the excess sure has helped me get stronger. Now it is time for me to back off a bit. I don't have a good way to measure my body fat accurately, but increase in strength has to mean something.