I don't know if it's 'hated' as much as it's fallen out of favor. C5's were clearly the best of the Customs for those of us who don't like ceramics and have a bunch of warm-toned guitars. And JB's were hit or miss. So out of the Duncan line, C5's were pretty good in our mahogany guitars. But when A8's became readily available, they gave us more output, more mids, less treble, and a great clean tone; in other words, a blend of the better qualities of the Custom, CC, and C5. Many guys here converted their's to C8's.
Several years ago Wymore dropped out, and Addicition FX stepped up and took his place as out main magnet supplier. He endeared himself to us by offering magnets most of us couldn't get before: UOA5's, RC A5's, RC A4's, RC A3's, and RC A2's. That spurred another round of magnet swaps. Those five new magnets have since become commonplace amongst Duncan forum members. The most unique is the UOA5, which sounds like a blend of A2 and A5, a middle ground many of us find desirable. For years I struggled getting enough bite of of some of my A2 HB's; UOA5's kept the A2 feel but added a little treble. Likewise, a number of A5 bridge HB's are pretty thin and bright. Again, an UOA5 fixed that, this time by adding warmth, mids, and texture. Voila! UOA5's are now residing in a variety of PAF's, medium output HB's, high output HB's, and P-90's.
There was always a 'need' for A8's, and for a long time C5's were as close as we could get. Many of us still would have liked a warmer C5 though. C8's solved that for most of us, but it's in-your-face output isn't always appreciated. That led to the UO C5 and C4, which give a more vintage sound by dialing down the output & adding dynamics and texture. Out of the six versions of the Custom (several more if you count roughcasts) there's at least one that'll please most players. They're not all equally popular but each has their following.
As for your being philosophical, consider this: manufacturers have to pick a magnet for their PU's, and it's almost always one they cuurrently keep in inventory. In reality, every HB has over10 different personalities (EQ's) depending on what magnet is in it. There's nothing sacred about the one the manufacturer happened to put in. Why not try some other magnets, after all, it's your PU. Often times it's that, or sell the PU. Think of the stock magnet as a one-size-fits-all kind of thing. As we all know, one size does not fit all with most products. A tailored suit will fit you better than one off-the-rack. So why not do that with a PU's tone? Especially since it only takes a few minutes and a few dollars. Maybe the manufacturer tested the PU in a certain kind of guitar design or wood, and you have something else. Or used different types of amps and pedals. Or maybe you don't like the tonal qualities of ceramics and want to put an alnico in? Or vice versa. Many reason why a replacement magnet may suit your style and gear better than the 'off-the-rack' magnet. Over the years I've seen posts from many guys who bought one PU after another trying to get the tones they wanted, and were frustrated and broke after the ordeal. This is the other end of the tone quest spectrum from mag swapping: living with less-than-ideal tones or selling lots of PU's. I've done both and think swapping mags is infinitely preferrable, and much cheaper. Same thing goes for guitars: we each have actions, set ups and string gauges we prefer. We almost always change what the guitar came with. Does that mean the guitar maker was 'wrong?' I imagine that I'm like most players, in that I play my best when I have tones I really like. That may mean tweaking some variables to get that, including PU's, pots, and magnets. Whether I'm on stage or at home practicing, I'm very glad that I've learned how to tweak those things. Doesn't mean there's anything 'wrong' with a PU, I just made it 'fit' me. I know that I have many more of Seymour's PU's than I would otherwise, because I've been able to change magnets and get the tones I want, and didn't have to look to another brand.