The two models are the same apart from the regular minibrute having the arp, and the SE having the sequencer.
You will be able to sequence either via USB or MIDI into your DAW of choice. You will also be able to control either via Silent Way, though, depending on how much CV you plan to use, and how often you plan to play the synth, you might actually choose the Microbrute, as it has more options for input/output via CV. For what it's worth, I have now owned all three, using Silent Way, Ableton Live, an Expert Sleepers ES-3mk3, and a eurorack synth. Of all three I highly prefer the Microbrute, for everything but the Minikeys. Since Arturia seems unwilling to make a Brute with the features of all three and I don't have the deskspace for all three, the Microbrute is the most versatile in my opinion for my studio.
Hope that helps.