Hy Jeevan,
I have tried to reproduce the same behavior in Vanilla organization but behavior is not reproducible. Steps which I followed as below :-
- Created the Custom Workflow
- Download the Plugin Registration tool(PRT)
- Logged into the PRT with the same user who is the owner of the workflow.
- Install the profiler
- Right click on Profile Plugin and Select Strat Profiling workflows
- Cklick on drop down and check above created workflow is present.
- Also created the new user
- Provide him system admin credentials
- Ask to log in PRT and check
- Different user is also able to see above created workflow.
Plugin registration tool version which I have used is as below :-

Next action which you can try:-
- Create a new workflow and check
- Download above PRT tool and check with that.