It’s a tricky question to answer but will try my best with knowledge gained from experts
Professional tax is something falling under the local governance and is recurring in nature - widely varies from state to state and there are some regions which do not have PT deductions too.
On the other hand ‘Gratuity’ is a central act and a conclusive one or once in a period payment where even the Supreme Court of INDIA has limited liabilities.
Now, considering this circumstance Gratuity is usually not considered for PT - because of its local governance and non-availability in some regions, where a central act cannot be merged.
Because of this special privilege, it even gets an IT exemption and stands as a benefit for the employee.
You may ask? is this mentioned in the law? State / local governance is very rarely mentioned in the central acts that too in the retirement (or) one-time payment acts, with Gratuity being a central act overruling all the other state acts it was not considered as a point while amendment.
And PT tends to change from state to state/region to region and is not uniform across INDIA.
This is a little tricky but logically this is the reason why PT (local governance) is not considered/merged along with Gratuity (central act) which is uniform across INDIA.