First point, under GST you will get input credit of every tax you pay on inward input supplies except few which are specifically mentioned.
You will get the credit of freight paid under RCM after payment of tax to government and return is filed by you.
You are at full liberty to either show the freight separately in invoice or you can add freight cost to cost of outward supplies.
Even if you show it separately recipient or buyer will get full credit of tax.
For invoicing you can use the invoicing application.