Not so sure on the chest one mate, logic would suggest though that the increased range of motion would increase the intensity!?
On the squat machine , do you front squat? When done correctly front squats will s*** over ANY machine squat! As they isolate the quads more than back squats they can and should be taken down to the point of your individual anatomical limit! Meaning sit down ALL the way! Even pause at the bottom for a moment to take out the rebound! Also do em the Olympic style. That is with the bar resting on upper pecs/ front delts with your arms bent back at the elbow, fingers just 'guiding' the bar in place ( shouldn't feel it in your wrists ). Keep elbows UP as this will rotate your scapula forward and under keeping your natural arch in mid/ lower back! Much easier to keep elbows up in this style than to keep shoulders/ forearms up in the arms crossed style!
Machine squats can be good for unilateral work as they obviously take the balance needed on one leg with a free wgt!