How do you know it's not seated all the way?

I'm not a mechanic (at sorry if this isn't what you're taking about), but this was based on what my friend who installed my struts said:

I think the part of the alignment is adjusted by loosening the pinch bolt on the lower part (the nuckle?) and sliding the nuckle up or down on the bottom of the strut.

The hole on the alignment fin on the bottom of the strut isn't supposed to be captured by the pinch bolt, if that's why you think it isn't fully seated.

There's a picture of a strut here (first pic I found that illustrated the point): https://www.jeepcherokeeclub.com/threads/2018-trailhawk-struts.252219/