Are CV boots designed to work only if they are in the "accordian" position? If one of the ridges was out of place and sticking down where it should be sticking up, could this cause premature tearing/wear?

Not normally. I've seen alot of boots like this, and have gone down the road for a long time. But I would imagine that after a prolonged amount of time that eventually the axle will put a hole in the boot from friction/movement. Do you know how old the boot is? This might dictate on how long it will last. it might be in this condition due to the fact of its age.

The boot is newly installed with the axle. Work was done by a local garage. Seems like they could have done a better job making sure it was seated properly.

probably squeezed some air out of it putting it on, has a slight vacuum in it, sucking in a ridge. not to worry about, more of an appearance thing