I want to have an alert 90 minutes before a calendar event. That isn't an option in Calendar on iOS. Fantistical has more alert time options than Calendar so I imagine there's a way to set an arbitrary alert time. Is there a way to do that from the command line or a script?
If you go into the Calendar app you can setup a custom alert per entry. Here I've added an item to my Calendar and then double clicked on it to open up a dialog to customize. Under that menu is an alert section under the time/date area of the calendar entry, in that menu select customize.Calendar entry dialog
CLI access to Calendar
You could use icalBuddy which was recommended in this other AD Q&A titled: Displaying calendar events as text, in the terminal.