Milestone depending on another milestome

Yes, you can do this.
And you can do this in two different ways :

1) When creating the dependency between milestones, you can add a delay between them.
Just set the delay to 90 days and you'll get exactly what you want

2) Another way to do this is to add a "Fixed duration" task between the milestones.
Fixed duration to 90 days, with do what you expect, with first milestone predecessor of task and second successor of it.
It is a bit longer, but will allow to represent why there is a gap between milestones.

Just pay attention that ProjeQtOr always consider "Open" days.