I think the only "real" mITX standard is the size of the board - there's certainly so standard on socket placement not the size/spacing of the mounting holes. As noted by a lot of the people on this forum, most of the HSFs for the Atom and Xeon-D models have been a not-very-common 51x51mm spacing. If you want to utilise one of these you're almost certainly going to need a custom mount, particularly if the stock heatpipes aren't in the right place. As with my streacom, you need to be very careful about mobo arrangement as well.
IIRC the HSF Supermicro use on some of their Xeon-D boards is the same P/N as that of the C3000 boards so the Cooljag should fit, but you'd want to check properly first. StH themselves did an article on aftermarket cooling solutions showing a couple of the other HSFs than fit the 51mm spec;
https://www.servethehome.com/aftermarket-cooling-for-the-supermicro-x10sdv-xeon-d-motherboards/
This does all feel a lot like square peg in a round hole or the tail wagging the dog though - if you were looking for an extremely low TDP unit for an existing case you should have said so
For the stated purpose though I'd be wary of using the C3000 for what you describe but your most important criteria seems to be being able to use your existing case.
Quick'n'dirty benchmark creating a tar.xz (not using pxz and defaulting to single thread) on the same dir (containing 238MB of FLAC files) on both machines;
Code:
effrafax@E3-1230v3:~$ time tar -c /path/to/flac/dir/|xz -c > /dev/null
tar: Removing leading `/' from member names
real 1m24.014s
user 1m23.780s
sys 0m0.484s
effrafax@C3758:~$ time tar -c /path/to/flac/dir/|xz -c > /dev/null
tar: Removing leading `/' from member names
real 2m49.212s
user 2m46.010s
sys 0m2.469s
C3758 is approx. half the speed of the Xeon in CPU-intensive single-threaded tasks like this. Switching to pxz to attempt to use all available cores;
Code:
effrafax@E3-1230v3:~$ time tar -c /path/to/flac/dir/|pxz -c > /dev/null
tar: Removing leading `/' from member names
real 0m20.390s
user 1m44.752s
sys 0m1.100s
effrafax@C3758:~$ time tar -c /path/to/flac/dir/|pxz -c > /dev/null
tar: Removing leading `/' from member names
real 0m36.750s
user 2m52.431s
sys 0m2.236s
4 cores vs. 8 narrows the gap considerably although the Atom is still performing at ~66% of the E3.
Edit: performing the same tests on an old Ivy Bridge 1265Lv2 (bought long ago for a TDP-limited project with base 2.5GHz and 3.5GHz boost clock);
Code:
effrafax@E3-1265L-v2:~$ time tar -c /path/to/flac/dir/|xz -c > /dev/null
tar: Removing leading `/' from member names
real 1m25.946s
user 1m25.840s
sys 0m0.736s
effrafax@E3-1265L-v2:~$ time tar -c /path/to/flac/dir/|pxz -c > /dev/null
tar: Removing leading `/' from member names
real 0m20.989s
user 1m51.668s
sys 0m1.364s
...and it's still faster than the C3000 and pretty much the same speed as the E3 v3 (no real surprise there). Long story short, I'd plump for a Xeon if I were you even if it means forking out for an expensive L model, especially if it means you won't need to fork out moolah on a custom-fitted cooling solution. But fitting any sort of desktop virtualisation server into a 35W TDP is a tall order IMHO.