albatross made very good points and saved me from typing them all out ^

Another point to consider is that many companies have corporate contracts that give a standard %off certain fare basis. E.g. 40% off a Y or B fare JFK-SFO. Perhaps the same for a C fare. The discounts are not offered on Z, or any other "lower" buckets. Therefore, UA keeps these prices artificially high, knowing that they have a captive audience to some extent--they also don't price themselves out of the market because anyone looking for a non-restricted ticket would just take the M fare.

What I have found is that whenever I see these "mispriced" (as you put it) fares on the market, the conclusion I have always come to boils down to "someone, somewhere is going to pay that fare" so UA might as well offer it.