I agree with some of what your saying and disagree with some.. especially the 'random' comment, as I'm definitely taking care and attention with my decisions..
Please go re-read. The "random" comment is referring to the fact that there are probably around two hundred different "standard" server boards that could be plausibly used as a FreeNAS server platform, and quite probably thousands of different chassis that one could try to fit things into. This is a huge combinatorial matrix and significantly impacts the likelihood anyone will happen to have your exact combination.
It seems I've overlooked/wasn't aware that 'E-ATX' is very flaky in the terms of it being a standard.
Sadly, it is indeed a bit flaky. This isn't really even limited to E-ATX. It is very easy to find people who order parts for a system and have a misadventure of some sort. My favorite is the tower cases with the PSU on the bottom, combined with PSU's with bottom-facing fans.
So I suppose I'm really bashing "E-ATX" and not supermicro although I do think they should be more clear with the mounting hole problem/differences. Just a single statement/warning on each products spec sheet would be enough.
I don't really see what the problem is. This is really just doing due diligence in putting together your system. The manufacturer's webpage for the Fractal chassis you listed has an interior chassis shot that clearly shows mounting hole positions, and you should just compare that to the Supermicro QRG I linked above. Make sure that you consider not just hole placement, but board overhang, cooler placement, fan airflow, PSU cabling, etc.
Also, it seems supermicro is the / one of the only decent /credible providers of enterprise-grade kit when going down the modular /build route rabbit-hole and not relying on hp / dell / ibm etc.
Correct. HP/Dell/IBM are heavily into their own OEM designs, which have some upsides, but also have a significant downside in that most of them assume a pile of disks need to be connected to a fancy RAID controller, and don't really let you BTO a system.
Of the companies that make credible {E-,etc,}ATX server boards, which is Tyan, Gigabyte, ASUS, ASRock, and Supermicro, only Supermicro is in this focused on the server market. The others all have a toe in the water but focus on PC and workstation boards.
Myself coming from a background where I have never tried to merge enterprise with consumer.. Ie, I've usually either gone out right enterprise proprietary kit prebuilt or the outright consumer gaming rig route when it comes to dealing with hardware.
The combination of needing enterprise hardware and consumer cooling... Seems to be a dark art, "a fun one all be it"
Correct. There are a number of common mistakes. One of the worst is underestimating airflow requirements. In a bid to make the quietest systems possible, people cheap out on the fans, and this can cause problems like HBA overheat when they don't get the airflow between the PCI cards right. This is something that isn't a problem in prebuilt kit, because someone did the engineering work, added lots of fans, and put in air shrouds to make the air go where needed.
The hobbyists have a terrible tendency to use the cheap fans from all these gamer-focused manufacturers (Noctua, Coolermaster, Phantek, etc), who build fans that are really only designed to last a few years -- you know, the average life of a gaming rig. Your NAS, however, is probably going to be running ten years or more.
So I hope you can realize my frustration and that my decisions on hardware weren't quick or random ones. I imagine a lot of people have found this out the expensive/hard way.
Right. I've been here for about a decade now, having written some of the earliest versions of the FreeNAS hardware guide. I build custom systems professionally, mostly for the data center, but also other stuff, so I've talked to a lot of folks about their builds.
This is why my opinion that you need to go look carefully at the components you're using is not a theoretical thing or just trying to blow you off. If you came to me and said that you wanted my shop to make you such a system, I would be going to have a very careful look at all the components you proposed, and see if it would be likely to work out. Here in the shop we do things ranging from custom cablework to 3D printing of parts, and it isn't really a big thing to drill a new position for a standout. But you can get your answer by doing what I suggested in my initial post in this thread -- get the pictures/diagrams and just LOOK.
Drilling cases is not for me I'm afraid. I think ill be looking into super micro standard single socket atx boards in the hope the mounting holes are good. And pass on the luxury of a dual CPU system.
What's the purpose of the dual CPU system, anyways? For a pure NAS, it is generally unnecessary. If you were going to host serious virtualization or jails, then it could be useful.