It's far better to begin with a free-standing squat, unloaded, and work your way up.
When you squat properly on your own, the muscles in your ankles, legs, hips and core work in tandem to stabilize and move the "load" (perhaps just your own bodyweight).
When you use the Smith machine, various stablizers are allowed to shut down, because that "control" you talked about above is being handled by the machine instead of yoru body.
As far as "safety", it's only unsafe to squat on your own if (a) your form is horrendous or (b) the load is too heavy. The really awful thing is that the Smith allows for bad form and improper loads. If you were to squat with 100lbs more than you should on a Smith and squat all the way down with bad form - on your toes, for example - you could actually do it, and maybe not feel that bad, because the Smith will assist you and keep the weight centered. If you tried that with a free squat, you'd destroy yourself.
So you say to yourself, "Sounds like the Smith is better beacuse I won't be able to "destroy myself"." This is where you have to realize that proper form and asking more of your stabilizing musculature actually promotes greater strength and growth!
I have no doubt that you can move up in weight and see some growth from using a Smith. However, I'm sure if you had started with a free squat and progressed from there, your results would've been even better!
Another, less concrete concept: relying on your own body for all of the balance and power in a lift creates a greater "body awareness". You think about your muscles differently, and feel them differently. This will actually carry over to other lifts.. thus leading to even more gains!
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