Following up my own post:
I first tried a Deep Silence 6 by Nanoxia, and while it was well built there's really no way to use more than 1 (3 slot) hot swap bay with it, the cooling wasn't great especially for the internal drive bays, and it is also enormous - not that I expected a small case, of course, given my E-ATX requirement and the number of drives I needed, but it was ridiculously big all the same and ironically, didn't make great use of all the extra space either - in fact I found it harder to work with than the case I ended up with. Luckily I was able to return it - Nanoxia support is pretty good.
Next, I found a Xigmatek Elysium Black on Ebay, new, for a good price. This case has 12x front bays, so 4x 3x5 hot-swap bays fit in it. It also fits E-ATX though I had to use 3 silicon motherboard standoffs at the top of my Supermicro X9DRE-LN4F motherboard - 6 mounts (including one in the center) fit but the holes didn't align for 2 at the top and 1 at the bottom. The silicon standoffs (old-school PC builders will remember those) worked fine and I didn't have to drill the case.
Good case overall, though I needed to add some sound deadening (SilverStone sells sheets of it for PC cases for $14) - not that it is loud with the right fans (I replaced all 3 stock case fans with Noctua PWMs controlled by my BMC), but the deadening helped quiet it all the way down. The case also has lots of open venting slots, particularly at the top, which made balancing airflow difficult and let the sound from the CPU fans at full rpm (also Noctua) escape easily. Cheap to remedy, at least, and not hard to install. Overall the case isn't outrageously big like the Deep Silence 6, has rubber grommets and plenty of tie downs, and overall was easier to get fitted out than the former in spite of being maybe 3/4 the size.
In fact, other than having to deaden it it'd be almost perfect for a large dual-Xeon tower case with all hot swap bays except for the fact they don't make them any more. You can find the remaining stock on Ebay (make an offer lower than advertised, they will take it trust me) but beyond that, you're out of luck. Which is too bad because tower cases like this that aren't obnoxious, fit weird Supermicro motherboards, and can handle 4 full hot-swap drive bays are unicorns these days.
Next, for the hot-swap bays I went with 4x Icy Dock Black Vortex MB074SP-1B and...well....
On the plus side, they have solid Sata III backplanes - power capacitors, sata power, no trouble with SSDs or large drives (I am using 10TB WD Reds) and the fans are in the front (and 120mm in size) so cool air blows in vs. being pulled in from the back of the cage. My drives run cool (37-40 under load - parity, preclear, etc. - and 29-32c idle), better than I've done with other cages in the past that have fans in the back. And the fans have removable dust filters in the front doors, which is convenient.
On the minus side, quality control is lacking with these; I had to swap one out for a dead drive light, and 2 of 4 filters didn't fit right, I had to bend the internal fan mounts out with a flat head. Also the stock fans are a little loud at full power and there's no temperature sensor/alarm, just a 3 position switch on the front. They are also blue LED, which I think looks dumb on a server (you can turn the light off, at least). I ended up replacing all 4 fans with Phantec high static pressure PWM fans; they are connected to my Supermicro BMC in a zone I set up just for the drives. Much quieter and same cooling performance, and also when the drives are idle you can't even tell they are on. And if one of the fans dies I get alerted.
The cages also have a bit of a funky design to them, though I found they blended well with my Elysium case. If I did it over I might not go with them again but that could just be because I had to do a lot of modding work (including stripping part of the nice cable braiding Phantec has on the wires so they wouldn't impede the door, and a bunch of other little things like that).
In any case I now have a dual E5-2697v2 server with 128gb memory, 8x10TB storage drives, 2x1TB ssd cache pool, and 1x1TB SSD for a passed through Windows VM game drive, in a case that fits next to my desk (though it isn't small by any means) and doesn't sound like a vacuum cleaner when running at full bore.
I'll write up more on this later with pictures if anyone is interested, though this probably isn't the right thread for that.