The patch-panel SEM plus Dark Energy is a great combo!
To answer some of your questions, yes you can use the built-in MIDI/CV converter of the DE to control your SEM. The DE's MIDI/CV converter is very limited, however, so eventually you will likely want something more flexible (Kenton Pro-Solo / Pro-2000, or Silent Way + compatible audio interface, etc.). As an example of the DE's limitations, resolution on the pitchbend MIDI>CV is very poor, and not very useful.
Personally I would not get a MIDI SEM. While it still sounds excellent, of course, and has a somewhat more robust built-in MIDI/CV converter tailor-made for the SEM, the lack of patch points would severely limit its use for me.
Although it's true, the SEM lacks attenuators for external CVs, you can still control the amount of modulation in some cases via the appropriate knobs.
All-in-all a great combo... with the added benefit of both using mini-jack patch cables ;-)