Gst invoice transportation

Yes, in case the service to persons for whom RCM is applicable, invoice has to be raised without GST while the invoice for customers whom RCM is not applicable, invoice has to be raised with GST

It is based on service specification
like Transport service under RCM, u may write RCM on invoice or if u have opted 12% then have to charge
and
in case of other services issue GST Invoice

Transporter has the following options:

1. 12% with ITC - Can charge GST @ 12% on all invoices and avail ITC on its inward supplies. RCM is not applicable for its customers if GTA has opted this option.

2. 5% without ITC - Customer pays GST under RCM wherever applicable. Transporter has to mention that RCM is applicable on its invoices. Transporter is not allowed to take ITC on its inward supplies.

Under any option, customer of transporter is eligible to avail ITC of GST paid on this GTA charges.

Transporter has to opt for any one of the above and cannot vary from customer to customer   

As per Notification 13/2017 CT (r) : GTA Services supplied to Registered Receptient , the Recepeint is liable pay GST on RCM .
As per Notification 12/2017 CT (R) : GTA can raise bill by charging 12% FC with ITC .

Note :
In both the condition the GTA is liable to raise the Bill & to Excercise the option of with ITC or without ITC need to opted beginning of FY & need to continue with same at end of Fy