Is the spacer located between the top of the strut and the body, or under the spring? If it's under the spring, it will make a VERY slight change in camber. If it's a body spacer, it won't affect alignment at all.
But, you're REALLY over-thinking this.
When you put the front of the car together, push the top of the struts to MAXIMUM negative camber. You want as much as you can get, and with most stock strut-suspension cars, you won't get much at all. So, just max it out. Get what you can get. If the two sides aren't close to the same (within 1/4 degree or so), maybe bring the more negative side in a little bit to match the other side.
Then reset the toe, because camber changes will throw the toe off, and that will cause tire wear issues, as well as maybe an off-center steering wheel.
Changing the front ride height is going to slightly change the weight distribution of the car, which will slightly affect the rear of the car. But, again, don't overthink it. You'll NEVER notice the difference that it makes.
FWIW, they're right, they can't just adjust camber. Camber effects caster and toe.