Low-bar was initially challenging for me too due to shoulders/tight pecs. They tightened up whenever I took a break from squats but flexibility will come back after a while. I agree that a light warm-up (some push ups, etc) is good to avoid pulling something in your shoulder when your focus is on the lower body during a squat. Keep in mind you only have to get close enough for a solid base...if the weight is secure on your back, no need to force another inch or two out of your grip width...
"You must have a very strong reason for doing an exercise. If you don't, scrap it and move on." -Jim Wendler