With the amount of force a caliper exerts when you put the boot in, any binding in the slot or pins should be very evident if it's enough to resist... unless there's a fairly large bit of superfluous crud between the caliper halves or behind the pad forcing them out of alignment then, if it were me, I'd take it out and do some spirited braking somewhere safe .... likely the 'high' bit of the outer pad nearest the hub will wear whatever small bit is needed to true the pad to the disc and give full sweep of the disc area.*
K
* what I'd do and what's 'proper' have been known to diverge! 🙂
