I agree 100% with your feelings of hostile reception with the FreeNAS crowd in the forums, as well as a clearly defined list of compatible hardware.
Don't take this as me coming to their defense, rather I am sharing my attitude toward trying to accept some of the nastiness. Some background on me first, I have a long history with the company that produces FreeNAS, so I know first hand that once "properly built", machines that run their code are some of the best machine experiences to have. I have experience with many open source systems going back before open source was viable in the 1980's. Further, my favorite open source network NAS was a FreeBSD system I customized myself. So a few years ago I had a situation where my wife wanted a network media server in the house, and I was sitting on a large pile of identical hard drives left over from a project. Like you I had experience with SATA multiplexors, and thought they would be useful at consuming all of my excess drives in a monstor home server using FreeNAS.
My first taste of discussing this on the FreeNAS forums was to encounter a culture of nay-sayers, always finding something bad to say about anything that was not done exactly how they did it. But I work around developers, and I have had my ideas laughed at and shot full of holes by their type many times. I have had GREAT ideas that launched revolutions, and in the beginning everyone laughed and told me I was an idiot for even trying... So I have a thickened skin for that sort of thing.
But that just caused me to stumble through my own process of discovery, using the many SATA muxes, and various HD controllers, trying to find a way to reliably consume an ungodly number of hard drives in one box. I prototyped my box over and over. I was using a chassis that could eventually hold 300+ hard drives and two motherboards that was left over from one of my companies I started based on my innovations... A souvenir of sorts... I tried two different SATA muxes I had experience with, and while everything worked, I was never impressed with the performance or the reliability. I had used SAS expenders blindly in the past, as they are generally built into the backplane of most enterprise servers. One day I had a server fail on another project, and as it was old we just scrapped it. While I was disassembling it to save some parts for the bench stock, I encountered the backplane, and saw that it was one of the fabled SAS expanders that someone on the FreeNAS users were always talking about. I decided to try and use it to see how it compared to the SATA muxes. My expectation was that it would be just like the SATA muxes. It didn't work with the first SATA Raid card I tried it with, but I read that it talked SAS, so I needed an SAS card. The 8-lane SAS cards were cheap compared to the sata raid cards I had piles of, so I decided to do the "FreeNAS forum approved" LSI card flashed to IT mode, just to see what it could do, compared to my end-to-end SATA rigs. What I saw was a vast improvement in performance and stability. Up to this point I thought my cables were flaky, or my power was bad, or even that something was crappy about the drives I was using. Switching to using SAS for my SATA drive infrastructure was eye-opening. SAS expanders are not multiplexors, instead they act like a asyncronous packet network connecting your drives to the OS in a way that makes an array of slow drives feel fast. The SAS infrastructure also seems to do error correction before the data hits the controller, so for example if you use a drive chassis that introduces errors, the SAS expander manages those errors and only forwards error free packets, freeing up the drive bus from problems caused by cheap hardware. I had stacks of rejected drive tray systems that were crapping out my SATA systems, but under SAS those trays seem to work flawlessly.
So what I discovered was that if you can look past the pompas attitude, and ignore the negative statements almost entirely, there is a lot of good wisdom being shared among those cranky forum users. They may not even know why the advice is good, only that it is.
Ignore the supermicro leanings, I found SuperMicro to be no better than anyone else. In my data center where I buy machines 30 at a time. The "identical" supermicro server systems acted like they were not identical at all, I found three sets of dissimilar behavior that could not be explained by firmware versions or hardware differences. Unlike other brands, they seem to be very inconsistent. If you buy one machine, you would never see this.
On the other hand, the LSI 9211-i8 advice is good, and should be followed. I'm using SAS expanders from random sources, and I'm not being too concerned about firmware versions, and they all seem to "just work" for me.
In the end measure, the compatibility issues are those of FreeBSD, so you should study the FreeBSD hardware guides for the more complete information. But to be fair, just because it is compatible doesn't mean it is good. And I have seen good working hardware abandoned by the FreeBSD kernel people, and I don't always agree with their reasoning. The FreeBSD community is filled with some of the same attitude you see in the FreeNAS community. But it is in those opinionated a$$holes you can get nugets of great information on how to build really nice systems. So think of them as your cranky uncle who can't keep a wife, but really knows how to build an excellent computer... Some people only have one skill, and it is not social.
The FreeNAS people don't know what doesn't work or why, they only know what worked or them.
If you have a small number of drives, and you have multiple backups, do anything you want. If your data is critical, and youwant a reliable server, at least use the LSI 9211-i8 advice, if nothing else. Your SATA muxes are fine and all, but for scalable performance make the switch to SAS, you won't be disappointed.