I do love it when we find an issue where we can disagree.
First, let me start out by saying that it should be a primary concern for all businesses to ensure that nothing in their practices discriminates against any person on the basis of race, gender, race, ethnic origins, sexual orientation, disability, etc. The type of fairness I'm talking about is not in the realm of this type of illegal and unethical injustice. That being said, you raise some interesting ideas in your post.
The idea of employee perception trumping all is an important one. But, if you let your company be run by employee perception and become a slave to it, I think you will be in trouble quickly. It's important to understand the significance of employee perception and then work to use that to create positive results.
An approach like pay transparency might seem like a good idea in concept but is often a train wreck in actual practice for a variety of reasons. Companies like Lominger who have studied performance and development have shown that we as individuals have a very warped sense of our own abilities and performance. As you would expect, most individuals will rate their own skills and abilities much higher than others will. Naturally, we are biased. Based on this "perception" of our value, we make a determination of the fairness of our compensation (by extension also inflated). Granted, in a few rare companies out there, pay transparency might work well, but in most places, it adds fuel to a already very hot fire.
In my opinion, productive fairness is achieved through clarity of expectation and consistency of practice. While our systems of measurement for employee performance are certainly flawed and incomplete, that doesn't mean that we don't know what matters and aren't able to recognize those things. The key is to clearly define and make apparent those things that matter and reward those things consistently. In regards to how we reward those things, I agree with you that organizations should pay more attention to what matters to their employees and reward them in ways that matter most.
For me, it boils down to this. People are not entitled to be treated how they perceive they should be treated at all times. Employers are entitled to create cultures and environments that (unfairly or not) reward certain types of behaviors and performance over others. Employees are entitled to leave and find another job when they find themselves at a company where they feel the situation is unfair. Employers are entitled to reward the things they think matter and to suffer the consequences. This is the balance in the system. In order for these circumstances to have a positive effect for the organization, there has to be clarity around what's expected and how that will be rewarded.
Done right, this system will feel very fair to the people who are making things happen to drive the business forward and will feel unfair to those who aren't. Businesses who reward the wrong things will find themselves out of business. That seems fair to me.
-Jason