GST Billing when Business source is aggregator

No you cannot.
Under this model, the OTAs normally collect payment from guests at the time of booking confirmation. The hotel will be entitled to an amount equal to the room rate minus/commission charged by the OTA. Following the guest check out (or any other time as agreed with the OTA), the OTA will remit the ‘Net Amount’ of revenue (after deducting the OTAs commission) to your account, and you may raise an invoice to the OTA with the net amount of revenue you are entitled to. So you cannot raise invoice to Customer.