Yeah I wonder how that affects the functioning of the muscle, if at all.
On the other hand some might argue that machines could perhaps supplment your training by emphasising parts of the muscle in ways that you cant with free weights. That would seem like a good argument, if true, and also if it's not overused.
I would not argue that it's a big deal if you are trying to get big and a little strong. You give a man enough time, food, resistance, and dianabol... he'll get there:). A muscle up to a certain point doesn't care if the resistance is from a barbell or a machine. my main problem is with something like a smith machine, something that locks you into such an un-natural plane of movement.
Free weight work simply allows more options. In my view, it it is always, whether free weight or machine, a bad idea to force un-natural form or technique on an athlete. At best it hampers an athlete's expression of strength/talent, at worst it leads to injury because an athlete is trying to force himself into a box he just doesn't naturally fit into. Best to let the athlete find his own groove.
You see this all the time with powerlifters and O/L lifters, people argue about xyz's form/technique and how bad it is. Meanwhile , the lifter has found his way to the top because he his own natural way of doing things(e.g. Patera, Rigert, Anderson, Peoples, Martinez, etc....) .
I think the real debate here isn't machines vs. free weight, in so much as it is proper implamentation and selection of machines in an athletes training.