Earlier quoted context omitted.
Kind of. As others have mentioned, the way you play an instrument is pretty important. It isn't hard to see the difference between playing a real harp and playing its software analog (no pun intended) on a keyboard. It may be a bit harder to understand how an actual modular synth is different if you have never spent any time playing one. Of course, the software based synths are more practical and easy to deal with si…
Yes, using the actual device gives some artistic freedom that's hard to control with a mouse and keyboard. Though you could try mapping some of it to a Midi instrument that allows for things like pitch bend (not sure if it's possible though)
Even something as seemingly inconsequential as the physical resistance in a knob can make a difference. For instance, I have one synth that has a very light filter cutoff knob and one that has a slow and heavy one. This tiny bit of tactile difference invites different kinds of uses. The light knob invites me to flick it rapidly -- the heavy one doesn't invite that kind of playing so you end up sweeping it more slowly.
I think the best example I've seen was a friend of mine playing a Doepfer Dark Energy synthesizer using a Dark Time sequencer. You can make the sequencer skip and jump by flipping switches to make it repeat a section or restart the sequence etc. So with without changing the pattern at all he made this entire performance just by creatively messing with the timing and playback.
This hadn't really occurred to me when playing similar instruments on a computer before. You would have had to make a very conscious decision to do exactly what he did in the software, but given the physical interface of the sequencer, this came naturally.