Dear memebr,
HRA is mandatory in CTC where it is part of the Minimum Wages Structure otherwise can be avoided.
However, the other major point is that if HRA will not reflected in Salary, the "HRA Exemption" can't be taken upto maximum permissible limit for computing the Income Tax.
If HRA is not part of CTC, still exemption can be taken, but that is restricted to some amount (may be 60 k per annum).
(For more detail pls refer to HRA exemption of IT Act).
Since, PF is not applicable on HRA, so it is advisable to show it in Salary structure.
Experience member can correct me.