Whichever method you apply, tax impact will be same.
You cannot charge 5% GST on freight. 5% is only for GTA and not for everyone.
You have to charge 18% on freight (same as your principal supply).
If you are showing Toll in invoice or not your total tax impact will be same.
In invoice you have to charge 18% on every expense. Status remain same even if you are issuing 2 invoices.