If I remember correctly, the reason Goodwill sometimes pays people under minimum wage is because they have a way to pay them per their performance so that they can employ less "efficient" people and not lose the efficiency in running their organization. Basically this way if they need two people to do the job that one person should be able to do, they don't have to pay double for it.
Another way to look at this is that in the workplace, you only have to accommodate employees's disability if they can do their job to capacity. For example, A person who is paralyzed from the waist down but mentally 100% and has use of their arms can do a job that's 100% sitting, like a desk/computer job. So you have to accommodate them in terms of providing a way for them to get to their desk, the bathroom, meetings, etc, in their wheelchair. You can't assign them an office on the 5th floor with no elevator. Etc.
However, a person who is paralyzed from the waist down probably cannot climb ladders or install light bulbs in the ceiling (I'm sorry in advance if you know someone in a wheelchair who can do this). So you don't have to accommodate them by calling someone else and paying extra every time a light bulb needs to be installed. You can just hire that other person who can change the lightbulb all the time and do all the other maintenance duties too. Wheelchair maintenance person is out of a job because employers don't have to give you a job, or keep you in your job if you can't do it.
Goodwill does not *have* to accommodate workers who are less than capacity because of their disabilities, but they do, and they take advantage of this federal law that allows them to pay them per their productivity rather than by the hour. I've read stuff where there were lots of examples where people worked for a couple of hours and wandered off for a couple of hours, or they didn't keep up a certain level of productivity. The oft cited person who was making 20 cents an hour or whatever, when you dig deeper into that, it's a person who was there all day but didn't do anything. If you do that in my workplace, you get fired. If you do that at Goodwill, you just get your pay docked. So they employ a lot of people who would otherwise be considered unemployable. Some of these people have chosen not to work at Goodwill but their other option is usually going on disability rather than working somewhere else for full wages. Some of the people choose to work at Goodwill because they like it, they would rather work than stay home, they are learning and improving, etc.
BTW, I didn't read all this stuff at the behest of the Goodwill. I read it all before I decided to volunteer for them because I had heard the same stuff everyone else had heard. But having volunteered for them, in Seattle at least I can say I have come to believe in their mission and their sincerity in helping people.
I can't even get into the topic of CEO salaries; if you compare CEO salaries of for-profits the size of Goodwill I am sure they would be much more than the CEO of Goodwill makes. But when you try to run an all-volunteer organization with an all-volunteer board, or even work for a small agency with shoestring salaries, let me know how that goes. I have done both and it's chaos and mayhem. The road to hell is paved with good intentions. Etc. You need people who know what they are doing at the top for the money and goods you donate to be used with diligence and accountability.
It's kind of ironic to have this discussion with mystery shoppers because I don't think we always make minimum wage, at least not in my city where minimum wage is $13 an hour now. Between looking for jobs, corresponding with schedulers and editors, completing the jobs, completing the reports, etc. I don't want to think about how little I make per hour mystery shopping.