Are protein efficiency ratio, net protein utilization, and biological value good indicators of quality protein for muscle building?
They are supposed to be, they were initially designed to be, but all of the protein assessment strategies/scales currently in use have their limitations.
These limitations start to materialise and become influential when the original populations that the scores are based on and derived from are altered and the formulas are applied to different populations.
For instance, one measurement that is most utilized and preferred by the majority of researchers in various fields as the most useful was not mentioned in your question, it is:
Protein Digestibility Corrected Amino Acid Score (PDCAAs)
In 1989, the Food & Agriculture Organization and World Health Organization (FAO/WHO) in a joint position stand stated that protein quality could be determined by expressing the content of the first limiting essential amino acid of the test protein as a percentage of the content of the same amino acid content in a reference pattern of essential amino acids (FAO/WHO, 1990). The reference values used were based upon the essential amino acids requirements of preschool-age children. The recommendation of the joint FAO/WHO statement was to take this reference value and correct it for true fecal digestibility of the test protein.
When this method is applied to the target group, i.e. preschool age children, it works. When applied to 70 year olds suffering from decreased kidney function (as blood test measurement for glomerular filtration rate GFR) , it doesn’t. Similarly, a problem arises if you’re looking at other subgroups of the population, not to mention high level athletes, or perhaps Champion Level Competitive Bodybuilders using various PEDs.
Practically speaking, unless you are doing research with the view to subsequently writing it all up in a peer reviewed journal, it probably really doesn’t matter much, even if the measurements are off by 25%+.
An example, say that you are a bodybuilder and you decide to roughly double your daily protein consumption using the following two supplements (Whey Protein Isolate and Casein):
WPI………………PER= 3.2 BV=104 NPU=92 PDCAAs=1.00
Casein………….PER= 2.5 BV= 77 NPU= 76 PDCAAs= 1.23
WPI is faster acting and has higher peak concentration of amino acids in the blood than casein.
If you are a healthy youngster, you’ll generally get a better effect with casein, if on the other hand, you are a healthy bodybuilder over 40, WPI looks to be more beneficial and show better lean muscle mass gains.
Why is this? Can these results be traced back to any of the values listed. Can any of these values explain the differing effects in the different age groups? And if so, how? The answer is no, not using these scales, at least not yet.
Also, if your current intake is say 50–60g a protein a day and you double that amount, you will most likely see a truly dramatic effect on your body composition. It wouldn’t matter much what the ratings of the protein source are that you choose to use.
But, the total effect on lean body tissue will not be so substantial if your current level is say 250g/day and you boost that to 500g/day. Protein quality may play a much greater role in this case, and the various formulas and numbers that they produce might start to take on increased significance.
So, things begin to change in the real word depending on the level of protein that you currently consume. None of the scales mentioned above take this observation into consideration.
Ah, but now we are beginning to move off topic a bit.
Footnotes:  Protein – Which is Best?