It can be difficult, but not impossible, to reward people differently for similar work. People can be hyper-alert to any treatment in the workplace that is perceived as unfair or unequal, and this is a drawback to the theories you make reference to. Assuming the validity of these theories, and I certainly subscribe to them, as a previous business person and presently, as a teacher, there are ways to make these theories work without having a disgruntled workforce.
Clearly, different kinds of people value different kinds of rewards, and to make matters even more complex, the same person might value different kinds of rewards at different points in his or her life. Some people value time, other people value money, while others might be most pleased with the closest parking place. As a young mother, I would have valued time more than any other reward, but now that I am older and getting closer to retirement, I would probably appreciate more money. This is not a function of my personality as much as it is a function of my needs at a particular time.
How can we give people what they want or need without causing a revolt? We can do so by understanding that any way in which we reward people is based upon recognition, an acknowledgement of a job well done. Given that basis, we can offer a menu of rewards, allowing people to choose which reward they want. It has become popular for workplaces to offer employees a menu of health care options or a menu of transportation options, so there is a precedent for this sort of menu. For example, one might offer paid time off, a free parking place, extra money, or bagels and cream cheese for a week. An employee who has choices is a much happier employee, and no one can complain about inequity in the reward system.