GST on subtransportation..??

Yes. It will.

3 parties are involved here. 

1. Main co who is taking service of Transporter.

2. Transporter giving sub contract to Sub-transporter

Hence, Sub-transporters GST will be paid by main party to whom original contract of transportation is given by the Service recipient co.

And main contractors GST portion will be paid by the co. under RCM.