To my view, a company should comply with all statutory norms; otherwise, the company would be punishable, and it is an offense according to statutory norms. In your case, the company has given a good salary structure, but they are not deducting either P.F. or P.T. according to norms.
Gratuity will not be deducted from an employee's salary. It will be paid at the time of retirement for eligible associates (according to the law, five years of continuous service).
About P.F., if a company does not have 20 employees or below, there is no need to register under the Provident Fund Act. If it crosses 20 or more employees, at that point, it should be registered under this act; else, it is an offense as per this act. Then the company should deduct P.F. (12%) from employees and has to contribute the same (12%) and should remit within stipulated dates.
If an employee's gross income is Rs. 15,000 or below, then the company should deduct ESI from employees at 1.75% of the gross salary and contribute 4.75% as per the ESI Act.
Similarly, the company should deduct P.T. (Professional Tax) as per respective state slabs and should pay as per norms within stipulated dates.
According to an employee's income, the company has to compute his total income, and it should deduct TDS (Income Tax) as per tax slabs.
I am wondering why this company is not deducting either P.F. or P.T. Of course, ESI and TDS will not be applicable for all associates since both depend on the salary range. I think you better ask about deductions from the concerned HR or Finance persons. If possible, you better go through the company website for basic information like when the company has started, the nature of business, number of employees, clients, and if possible, ask any present working employees; that would give more information.
This is only my view; the decision is yours. If you wait some more time, our seniors will give you an appropriate answer.
I wish you all the best & God bless you.