Ok...as far as the rear axle affecting the position of the front axle? I'm throwing the BS flag there.
If the front axle is sticking out farther on one side than the other, the axle is/has shifted to the left with the lift. The adjustable track bar should allow enough adjustment to pull the axle back underneath and recenter it (thats what its designed for). Once that is done, then they will have to start all over again with the alignment.
Now, part of what he said is true. The position of the rear axle will affect how it drives/steers, and how the front has to be set to counteract any irregularities in regards to where the rear tires are pushing
the Jeep- (square it up) to use his wording.
As fas as adjustable control arms go, they do have the benefit of infinite adjustability and you'll be able to dial that alignment in damn near perfect, but you still need to recenter the front axle and the control arms won't do that for you.
Call around to other shops. See if anybody specializes in lifted/lowered suspension alignment and get prices. If you've found the only place in your area, well, might have to work with them to get things straight. (no pun intended)