Not specifically true to the exception of kids and girls always. I'm in the 300+/450+/450+ club all for reps of no less than 5, by no means great numbers compared to many; however, I have used machines for 3-6 months at points during rehab from car injuries, sports injuries, etc. The hammer press, hammer strength, leg curl, seated leg curls, shoulder presses, assisted pull up, leg press, abduc adduc, pulley, lat pull down, seated row, cable cross over, all are considered machines in my book. If it is connected to an apparatus then it is a machine though cables are quite different than being "stuck" in a specific position like traditional machines where they allow more natural movements.
But machines are typically less stressful on the body with a few exceptions of which smith squats is one of several. They are overall safer. I agree with you though, they can put your body into unnatural positions but that depends on the machine itself. All machines are not made the same. Different gyms will have very different equipment. I can vouch for several machines that kill my tendons at one gym yet give me NO pain at my other gyms. Several individuals that I train will say the same. It is all in the construction and leveraging system. I would NEVER advocate JUST using machines unless you are in a injured state or just learning some basics exercise routines for the first time. I would rather someone start with free weights.
Bodybuilders have used machines very often for decades, both natural and enhanced bodybuilders. Professional athletes use them consistently throughout the season. I once worked for the Atlanta Falcons franchise, I have seen these guys use machines on a constant basis. I love free-weights, don't get me wrong but I am just saying there is a place for them in all routines if someone chooses to use them.
Free weights do promote true strength and balance due to taxing the CNS, strengthening tendons and teaching us how to recruit motor units for a lift, I will agree 100% with you there. But, using a machine in your routine isn't going to magically rob you of anything.