I've heard folks here recommending UNAS 810A. I don't have any experience. It will be a tight fit for MATX and you will need ribbon cables for PCIe.
I really like the UNAS 810A. It is very compact, can run quiet (see below) and looks good enough to leave out in plain sight.
It does a GREAT job cooling the drive cage area, but other people have noted that the airflow around the MB area is poor. This is valid complaint, so running anything that gets hot is not practical. Also, if you do run any expansion cards you need to use a flex riser (UNAS sells one). The riser works well, but it tends to block what little airflow is available. And if you need BOTH available expansion cards it gets pretty challenging to fold-in two risers without completely blocking air across the MB. There is also very little to no room for any kind of tall aftermarket HSF options.
I happen use an X11SSH-TF motherboard with lower-power CPU (E3-1240L v5). Having 8 SATA and 10Gbe on-board means no need for any expansion cards. This setup works well for me and runs very cool. I have run it with higher-clock CPUs with no problem (E3-1270v6) but as a pretty pure NAS I never needed the extra compute.
Making it quiet does take a little bit of work. The large rear fans are OK, but I did swap them for Noctua PWM fans. The real noise culprit is the thin fan on the side. As shipped, this is a high speed 3-pin fan that runs pretty loud. Its non-PWM so slowing it takes a bit of work. You can either use a resistor mod (I used the connectors that came with the Noctua fans) or you can search for a PWM fan and slow it down from the MB controls - though finding a suitable PWM fan the right size can be challenging (70x15, IIRC, but I could be off - its been a long time).
Overall I really like and recommend this case. But you should look around at other reviews because there are folks that really don't like it too and they express some valid concerns.
I've considered upgrading to an E2200 based configuration (mainly to sell and reclaim value from the X11SSH/E3 while it still has solid resale value). But to date I have not found a suitable MB for this current generation with all the right boxes ticked - mATX or uITX, 8 onboard SATA, onboard 10Gbe and IPMI.