The problem is the locating features of the knuckle to the strut usually has a bit of play in it - they can't be 100% perfect or they wouldn't go together. Some cars specifically use that as an adjustment point, some cars try to keep it tight. Even if everything is perfect, there are manufacturing variances that will likely end up putting the knuckle at a slightly different location than previously.
Alignment definitely should be checked after any suspension part replacement. You have a really good case that it should be included because, just like you said, it's a required activity after doing the warranty work. Spend some time yelling at the manager, especially now that they're taking extra time, and they'll likely write it off. If not, do the whole "I'll go talk to the GM and make it clear this is ridiculous and I'll never come here again..." stuff.
It's a major PITA, but you usually have to be a jerk to dealers to get them to do the right thing. It's like mutually assured destruction - they do stupid things because customers are jerks, and customers are jerks because they do stupid things.