Hi Deepti, I am happy to help!

The system will natively close out parent objects if all of their child items are marked complete. This is why you are seeing the Milestone and Project getting marked complete when your only task is marked complete. 

To get around this auto-close functionality myself, I add a Milestone to all new Projects with Milestone Type = Project Closure, that way there is a child item that remains open on the project. You can add additional validation to stop the manual closure of this milestone if you use a Custom Action form for project closure today. 

Based on the information you provided, I recommend creating a Project template for each of your ‘Project Types’ which would include all (or most) the milestones required for that Project Type - your PMs can later add Milestone Templates as necessary to finalize their project plan. Then, within your new Project form, you could include criteria that looks at Project Type to apply the appropriate project template. 

Creating Workflow rules that evaluate when a Task is completed in order to add a new Milestone can get tricky as you would need to figure out how to tell the system which Task to evaluate if there are multiple (Task Type potentially) and if you are looking at 5 separate milestones, this could potentially result in 5 different Task Types and evaluation criteria for each situation. 

Hope this helps!

Mikayla