I own the military version. The main differences I recall is no external frequency counting capability and no frequency lock capability. Other than that, it has the same amplitude and frequency modulation functions, same frequency ranges (may or may not include the frequency doubler option to extend the range up to 1 GHz).
I believe it has the same phase noise spec. I recall I measured mine when I got it and it was within the civilian phase noise specifications.
Both the civilian and military versions do have different options, so your mileage may vary.
The military version does have the distinct advantage of being colored bright yellow, so you'll never miss it in the dark.