No, the arm isn't attached to the strut at the LCA that would affect alignment (one bolt through it.) Your alignment was probably out because of the replacement of the LCA itself, which will affect everything.
It takes longer to put the car up on stands than to get the strut out imho, lol... (esp. on my lowered car!) A paint touch up container with the lil brush work great for this as you can get right around the whole mount easy.
Only real hard part is the lower bolt, as they can be a pita to get out sometimes, and you need to tighten it with the weight of the car on it.
This would be easier for a stock height car here too as you wouldn't need to keep jacking it up, just pop the wheels on, turn the air ride switch on and let it level, and drive it up some ramps and tighten.
On mine, the lower bolt I snug it up lightly, then jack the front up real high and slid wheel ramps under the wheels, turn the air ride switch on to fill the bags, and tighten them then. I turn the air ride switch off again and jack it up off the ramps and drop it, as I can't drive off them as the car is too low...