Normally in any offer of appointment, however small the organisation may be, they will men tion that PF & Gratuity would be as per rules. As the eligibility of gratuity starts after completion of 5 years service, question does not araise to add in the ctc at the time of initial appointment. As the gratuity will be paid on Basic Pay + DA , some of the companies arrive notional Basic + DA at the time of initial appointment it self, so that no ambiguity is faced while arriving gratuity amount at the time of payment at a later date.
The rule of taking the service of 6 months or above as completed year of service for gratuity purpose will be applicable only after completion of first 5years service but not to fill the gap of 5 years. Perhaps, your employer took this wild decision of sending you out, only to avoid gratuity.