The limited pool of questions is an issue with some of the newer exams. MD-100 currently has 145 questions in the pool. They usually add more over time. When you take the practice exam, you can choose custom quiz, where there is an option to include only unused questions. This will help a little, but you will still run out of questions eventually.
I will share my strategy for using practice exams, that I have found over the years to be effective. I think you have a pretty good grasp on this, but I wanted to post all of this for others that might have the same questions/concerns.
Start with a custom quiz. With this exam there are four domains. So I would do 20-30 questions. With a pool of 145 questions, this would allow me to take the practice exam 5-7 times without repeating questions. This should also give me 5+ questions per domain, so a decent cross section. Choose the option to show answers and explanations.
For each question, read the question, read the answers, and then read the question again. That way, the second time I read the question, I know what the possible answers are. (I use this same strategy in the exam booth) Pick the best answer. Then read the explanations. Read why the right answer is right, but also read why the wrong answers are wrong. I have learned many things that have paid off in other questions using this method.
If I have any misunderstandings about the explanations (right or wrong answers), I stop and do some research. I don't move on to the next question, till I feel comfortable with the information. This is another reason for limiting the number of questions, it would take to long and I would end up stopping the practice exam ;) I also don't want to see all the questions yet!
Once I finish the exam, I look at my score. I'm not concerned with the actual score, I just want to see what areas I need to focus my study time. Next I go study, Fire up some Practice Labs. Click on everything, try things, even if they are not mentioned in the Practice Labs instructions, explore. If something is confusing, stop and research it.
Now it's time to try the practice exam again. I use the same exam settings, making sure to choose to not repeat questions I've seen before. (Another reason for only doing 20-30 questions, I should be able to take the practice exam several times without seeing the same question twice.) Hopefully this time, I have to stop and do research much less. If I do pretty well, I might now try the practice exam in certification mode (timed and no answers) This is where if I get 80%, I feel like I'm probably ready. If I don't do well, I look at where I need to study, and once I feel ready, I try the exam in certification mode again. Because I did a limited number of questions, I should still be seeing new questions.
The key points to remember is to use the practice exams as a means of determining where you need to spend more time. This makes your study time more effective. Taking the practice exam over and over till you score well is just testing your memorization skills. That won't help, since these are not the questions you will see on the exam.
Believe me, I too wish there was more guidance on how deep we should go on each subject.
Good luck on the exam! I welcome your feedback, as I want to make the best course possible!