Not so much that anything is wrong with PowerEdge servers as I've got a bunch of them in varying offices. It's just their pricing is off the freaking wall these days. I wish I could say they were nickel and dimeing people but they are Grant and Benjamin'ing for small things. I had this issue before for more price conscious customers and what would have cost almost 6k with Dell ended up costing then $2800 with me building, and that was with my markup. We also got better parts, just didn't have hot swap bays which was ok for them.
The guy at sales from Dell couldn't really help me, so he took my info and is passing it onto someone else who can and will supposedly call me tomorrow morning. Sad, I kept asking if anyone else there could help me but he made it sound like she was the only one!? So Dell, who has over 35,000 employees, this one lady is the ONLY person who can help me price out a server properly? OK, totally makes sense.
I never, ever take their first quote. I generally configure what I need on Dell Premier, and then tell them they have to do better on the price. However, I do work in education and they cater to us like you wouldn't believe. That $6,000 for you would probably be $4,000 or less for me...before I go to them for further discounts.
That said, their cost is higher than rolling your own because they are guaranteeing and testing their solution from front to back, top to bottom. That also probably included several years of support, which also includes replacement parts (and a technician to come onsite to replace said parts, if you so request it). There's something to be said for having that piece of mind. Check your quote, too...some of the sales guys will sneak in the highest level of support and that will jack the price by a lot. If you're redundant enough then you can likely get away with next-business day. What I get all depends on what the piece of equipment is doing, or if it's a cluster of servers where if one of them completely fails we're still operational.
With regards to SuperMicro, I've used various things from them over the years. A lot of appliances "created" by system vendors are actually rebranded Supermicro boxes. Case in point, the Polycom MCU and Capture appliances we recently acquired. I do use their hot-swap bays in my personal server at home. I've had two of them going strong for about 8 years or so now. They've gone through multiple drive upgrades, to include from SATA to SAS. You are correct in that it's not a port multiplier style backplane, it's an individual port per drive. I have my drives connected to an LSI/Avago/Broadcom (it's changed hands several times the last few years) RAID controller using SFF-8087 breakout cables.