Difference between native automation rules and analytic rule automation rules?

Herber62 For the first part of your question, why can't we select automation rules within an Analytic rule, it is basically a design decision.   You can always ask for this to be added via the User Voice site: Microsoft Sentinel · Community (azure.com)

For the second question, you can easily select which Analytic rules the Automation rule works against.  When adding/editing an Automation rule, in the "Conditions" section, is a dropdown list called "If Analytic rule name" and the default values are "Contains" and "All".   If you click on the "All" you will see it lists all the rules you have and you can selected one or more.   Then the automation rule will only trigger when one of the selected Analytic rules creates and incident.   You can also use this feature to take care of your first question.