My 11 week old knows the following commands and how to perform them:
2. Stay (2-3 seconds)
3. Lay Down
4. Go in your crate.
5. Drop it
7. Lets go (walk with me)
I know he knows these because when I am about to give him an extremely tasty treat he obeys them 100% willingly and will do ANYTHING for the treat.
however, when there is a less tasty treat involved or no treat at all and just praising (good boy) he 50/50 follows them, sometimes ignoring me completely.
At his age it's highly unlikely that he truly KNOWS all those commands. If he's not doing them all the time, no matter the circumstances, then he hasn't fully generalized them. Test your sit command - will he sit across the room from you? Will he sit if you tell him to while you're laying in bed, sitting in a chair or on the floor? With your back turned? When he's in the car, at the vets office, walking near a busy street? In every room in your house at any time of day? Even if he will do that, he may not be able to comply around heavy distractions, so you'd need to train under those conditions too. Any time you make it more challenging you should lower your criteria accordingly and work your way back up, and your rate of reinforcement should reflect that.
Is this just protest because he is young or does he have no respect?
Yes, it's because he's young, but no, it has nothing to do with protesting or lack of respect, any more than a 6 month old human baby is capable of protesting or not respecting it's parents. That's about the developmental level of an 11 week old puppy and neither is capable of such complex feelings or behavior.
Is he challenging me as alpha? Will he grow out of this or do I need to do something different?
No, he is not challenging you, nor is he trying to be alpha. Dogs really don't simply "grow out" of anything. Maturity will help, as his attention span increases, but training will still be necessary. One important thing that you can do differently is to just lower your expectations. Keeping them reasonable based on what a young puppy is actually capable of will leave you less frustrated and make training and life in general more fun for both of you.