I've a few questions.
1.
Do all VO2 Max tests give the energy source breakdown, or might some just tell you the overall oxygen consumption?
I dunno, but here is one guys tests...The interplay of exercise and ketosis You may have to read part II for the VO2 max stuff.
2. If one stayed low carb, does the body maintain a certain amount of muscle glycogen storage through glyconeogenesis, or are the muscles left almost completely "empty"?
Yes, it will still prioritize to produce and refill gycogen stores.
3. Can glycogen from the liver be moved quickly (or at all) into the blood stream for muscle work in the absense of sufficient muscle glycogen?
From what I gather...yes it will be mobilized when appropriate.
4. Is there a good generalization about when gluconeogensis would use dietary protein, rather than muscle mass to do its thing?
Would most (gluconeogensis) occur after a protein meal and top up liver stores?
Sure...as long as you are consuming enough protein in the diet and doing some resistance training to preserve muscle mass this occurs.
On a side note, my understanding was that "preferred fuel" means what the body will prioritize, not what it "likes" the best.
For example ethanol is burnt before carbohydrate. Technically it's "preferred" over carbs, it doesn't mean you should go on a high alcohol, low carb diet
Damn the high alcohol low carb diet is my favorite one too!