Yes, you get the idea. That's how they align real cars' wheels, only they use lasers instead of rulers.
Yes it will.
That's why you don't.
The idea however is to get this misalignment to be as small as possible (you can only have zero if you don't have any suspension).
This is what you're practically trying to achieve.
Equal misalignment at fully compressed suspension and at fully extended suspension. At the same time, this misalignment has to be the absolute minimum it can be.
This will only happen if you have the steering rod outer end (the part attached to the steering block) travel equally up and down (as the suspension travels between full droop and full compression) when compared to the inner end (the end attached to the steering/drag link).
This might mean that you have to shim the balljoints at both ends of the steering rod.
Team Greasy Weasel
The best upgrade to any car is some driver skill.